HEADER IMMUNE SYSTEM 28-FEB-24 8S6V TITLE CRYSTAL STRUCTURE OF FAB-2D9 CHIMERA COMPLEXED TO A BIS-TN TITLE 2 GLYCOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: G2D11 (VH-CH1); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPND 6 QVQLQQSDAELVKPGASVKISCKASGYIFADHAIHWVKRKPEQGLEWIGYISPGNDDIKYNEKFKGKAT COMPND 7 LTADKSSSTAYMQLNSLTSEDSAVYFCKRSLPGTFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNS COMPND 8 MVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASS COMPND 9 TKVDKKIVP; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 2D9 (VL-CL); COMPND 12 CHAIN: B, D; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: COMPND 15 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSDQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFT COMPND 16 GSGSGTDFTLTISSVKAEDLAVYYCQQCYSYPFTFGSGTKLERKRADAAPTVSIFPPSSEQLTSGGASV COMPND 17 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTS COMPND 18 TSPIVKSFNR; COMPND 19 MOL_ID: 3; COMPND 20 MOLECULE: MUCIN-1 SUBUNIT ALPHA; COMPND 21 CHAIN: M, N; COMPND 22 SYNONYM: MUC1-NT,MUC1-ALPHA; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS MONOCLONAL ANTIBODY, FAB-2D9, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.HURTADO-GUERRERO,J.MACIAS-LEON,A.GONZALEZ-RAMIREZ REVDAT 1 25-JUN-25 8S6V 0 JRNL AUTH R.HURTADO-GUERRERO,S.GATOS,I.GINES-ALCOBER,J.MACIAS-LEON, JRNL AUTH 2 A.MANUEL GONZALEZ-RAMIREZ,I.KASAPOGLU,B.VELOZ,I.COMPANON, JRNL AUTH 3 M.GHIRARDELLO,P.MERINO,F.CORZANA,O.BLIXT JRNL TITL RECOGNIZING TN AND STN EPITOPES IN PROTEIN CONTEXT: JRNL TITL 2 STRUCTURAL ADVANCES IN PHAGE DISPLAY LIBRARIES FOR JRNL TITL 3 TUMOR-SPECIFIC ANTIBODY DISCOVERY JRNL REF NAT.CHEM.BIOL. 2025 JRNL REFN ESSN 1552-4469 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 71315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 3113 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5207 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 216 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 125 REMARK 3 SOLVENT ATOMS : 521 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : -2.64000 REMARK 3 B33 (A**2) : 2.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.050 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6993 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6194 ; 0.004 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9517 ; 1.445 ; 1.683 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14558 ; 0.782 ; 1.607 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 860 ; 7.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 18 ; 8.056 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1109 ;16.636 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1080 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7679 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1317 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3434 ; 2.333 ; 3.063 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3434 ; 2.332 ; 3.062 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4281 ; 3.361 ; 4.571 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4282 ; 3.362 ; 4.572 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3559 ; 3.439 ; 3.417 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3540 ; 3.371 ; 3.404 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5202 ; 5.073 ; 4.965 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7547 ; 6.781 ;44.230 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7433 ; 6.668 ;43.279 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8S6V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 134.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE BIS-TRIS PEG 3350, PH REMARK 280 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 33.52650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.48100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.77300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.48100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.52650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.77300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, M REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, N REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 GLN A 131 REMARK 465 THR A 132 REMARK 465 SER C 128 REMARK 465 ALA C 129 REMARK 465 ALA C 130 REMARK 465 GLN C 131 REMARK 465 THR C 132 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG D 108 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG D 108 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 PRO N 2 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 95 -166.92 68.91 REMARK 500 ALA B 51 -36.46 71.15 REMARK 500 SER B 77 75.52 47.62 REMARK 500 ALA C 88 176.48 179.67 REMARK 500 SER C 95 -168.67 68.26 REMARK 500 ALA D 51 -33.92 69.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 106 0.11 SIDE CHAIN REMARK 500 ARG C 39 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8S6V A 1 212 PDB 8S6V 8S6V 1 212 DBREF 8S6V B 1 211 PDB 8S6V 8S6V 1 211 DBREF 8S6V C 1 212 PDB 8S6V 8S6V 1 212 DBREF 8S6V D 1 211 PDB 8S6V 8S6V 1 211 DBREF 8S6V M 1 9 UNP P15941 MUC1_HUMAN 127 135 DBREF 8S6V N 1 9 UNP P15941 MUC1_HUMAN 127 135 SEQADV 8S6V NH2 M 10 UNP P15941 AMIDATION SEQADV 8S6V NH2 N 10 UNP P15941 AMIDATION SEQRES 1 A 216 GLN VAL GLN LEU GLN GLN SER ASP ALA GLU LEU VAL LYS SEQRES 2 A 216 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 A 216 TYR ILE PHE ALA ASP HIS ALA ILE HIS TRP VAL LYS ARG SEQRES 4 A 216 LYS PRO GLU GLN GLY LEU GLU TRP ILE GLY TYR ILE SER SEQRES 5 A 216 PRO GLY ASN ASP ASP ILE LYS TYR ASN GLU LYS PHE LYS SEQRES 6 A 216 GLY LYS ALA THR LEU THR ALA ASP LYS SER SER SER THR SEQRES 7 A 216 ALA TYR MET GLN LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 A 216 ALA VAL TYR PHE CYS LYS ARG SER LEU PRO GLY THR PHE SEQRES 9 A 216 ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SER SEQRES 10 A 216 ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO SEQRES 11 A 216 GLY SER ALA ALA GLN THR ASN SER MET VAL THR LEU GLY SEQRES 12 A 216 CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 A 216 THR TRP ASN SER GLY SER LEU SER SER GLY VAL HIS THR SEQRES 14 A 216 PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SER SEQRES 15 A 216 SER SER VAL THR VAL PRO SER SER THR TRP PRO SER GLU SEQRES 16 A 216 THR VAL THR CYS ASN VAL ALA HIS PRO ALA SER SER THR SEQRES 17 A 216 LYS VAL ASP LYS LYS ILE VAL PRO SEQRES 1 B 217 ASP ILE VAL MET SER GLN SER PRO SER SER LEU ALA VAL SEQRES 2 B 217 SER VAL GLY GLU LYS VAL THR MET SER CYS LYS SER SER SEQRES 3 B 217 GLN SER LEU LEU TYR SER SER ASP GLN LYS ASN TYR LEU SEQRES 4 B 217 ALA TRP TYR GLN GLN LYS PRO GLY GLN SER PRO LYS LEU SEQRES 5 B 217 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 B 217 ASP ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 B 217 LEU THR ILE SER SER VAL LYS ALA GLU ASP LEU ALA VAL SEQRES 8 B 217 TYR TYR CYS GLN GLN CYS TYR SER TYR PRO PHE THR PHE SEQRES 9 B 217 GLY SER GLY THR LYS LEU GLU ARG LYS ARG ALA ASP ALA SEQRES 10 B 217 ALA PRO THR VAL SER ILE PHE PRO PRO SER SER GLU GLN SEQRES 11 B 217 LEU THR SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN SEQRES 12 B 217 ASN PHE TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE SEQRES 13 B 217 ASP GLY SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP SEQRES 14 B 217 THR ASP GLN ASP SER LYS ASP SER THR TYR SER MET SER SEQRES 15 B 217 SER THR LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS SEQRES 16 B 217 ASN SER TYR THR CYS GLU ALA THR HIS LYS THR SER THR SEQRES 17 B 217 SER PRO ILE VAL LYS SER PHE ASN ARG SEQRES 1 C 216 GLN VAL GLN LEU GLN GLN SER ASP ALA GLU LEU VAL LYS SEQRES 2 C 216 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 C 216 TYR ILE PHE ALA ASP HIS ALA ILE HIS TRP VAL LYS ARG SEQRES 4 C 216 LYS PRO GLU GLN GLY LEU GLU TRP ILE GLY TYR ILE SER SEQRES 5 C 216 PRO GLY ASN ASP ASP ILE LYS TYR ASN GLU LYS PHE LYS SEQRES 6 C 216 GLY LYS ALA THR LEU THR ALA ASP LYS SER SER SER THR SEQRES 7 C 216 ALA TYR MET GLN LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 C 216 ALA VAL TYR PHE CYS LYS ARG SER LEU PRO GLY THR PHE SEQRES 9 C 216 ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SER SEQRES 10 C 216 ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO SEQRES 11 C 216 GLY SER ALA ALA GLN THR ASN SER MET VAL THR LEU GLY SEQRES 12 C 216 CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 C 216 THR TRP ASN SER GLY SER LEU SER SER GLY VAL HIS THR SEQRES 14 C 216 PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SER SEQRES 15 C 216 SER SER VAL THR VAL PRO SER SER THR TRP PRO SER GLU SEQRES 16 C 216 THR VAL THR CYS ASN VAL ALA HIS PRO ALA SER SER THR SEQRES 17 C 216 LYS VAL ASP LYS LYS ILE VAL PRO SEQRES 1 D 217 ASP ILE VAL MET SER GLN SER PRO SER SER LEU ALA VAL SEQRES 2 D 217 SER VAL GLY GLU LYS VAL THR MET SER CYS LYS SER SER SEQRES 3 D 217 GLN SER LEU LEU TYR SER SER ASP GLN LYS ASN TYR LEU SEQRES 4 D 217 ALA TRP TYR GLN GLN LYS PRO GLY GLN SER PRO LYS LEU SEQRES 5 D 217 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 D 217 ASP ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 D 217 LEU THR ILE SER SER VAL LYS ALA GLU ASP LEU ALA VAL SEQRES 8 D 217 TYR TYR CYS GLN GLN CYS TYR SER TYR PRO PHE THR PHE SEQRES 9 D 217 GLY SER GLY THR LYS LEU GLU ARG LYS ARG ALA ASP ALA SEQRES 10 D 217 ALA PRO THR VAL SER ILE PHE PRO PRO SER SER GLU GLN SEQRES 11 D 217 LEU THR SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN SEQRES 12 D 217 ASN PHE TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE SEQRES 13 D 217 ASP GLY SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP SEQRES 14 D 217 THR ASP GLN ASP SER LYS ASP SER THR TYR SER MET SER SEQRES 15 D 217 SER THR LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS SEQRES 16 D 217 ASN SER TYR THR CYS GLU ALA THR HIS LYS THR SER THR SEQRES 17 D 217 SER PRO ILE VAL LYS SER PHE ASN ARG SEQRES 1 M 10 ALA PRO GLY SER THR ALA PRO PRO ALA NH2 SEQRES 1 N 10 ALA PRO GLY SER THR ALA PRO PRO ALA NH2 HET NH2 M 10 1 HET NH2 N 10 1 HET EDO A 301 4 HET EDO A 302 4 HET SO4 A 303 5 HET EDO B 301 4 HET EDO B 302 4 HET SO4 B 303 5 HET EDO C 301 4 HET EDO C 302 4 HET EDO C 303 4 HET SO4 C 304 5 HET EDO D 301 4 HET EDO D 302 4 HET EDO D 303 4 HET EDO D 304 4 HET SO4 D 305 5 HET SO4 D 306 5 HET A2G M 101 14 HET A2G M 102 14 HET A2G N 101 14 HET A2G N 102 14 HETNAM NH2 AMINO GROUP HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN EDO ETHYLENE GLYCOL HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 5 NH2 2(H2 N) FORMUL 7 EDO 11(C2 H6 O2) FORMUL 9 SO4 5(O4 S 2-) FORMUL 23 A2G 4(C8 H15 N O6) FORMUL 27 HOH *521(H2 O) HELIX 1 AA1 ILE A 28 HIS A 32 5 5 HELIX 2 AA2 GLU A 61 LYS A 64 5 4 HELIX 3 AA3 LYS A 73 SER A 75 5 3 HELIX 4 AA4 THR A 83 SER A 87 5 5 HELIX 5 AA5 SER A 156 SER A 158 5 3 HELIX 6 AA6 SER A 186 TRP A 188 5 3 HELIX 7 AA7 PRO A 200 SER A 203 5 4 HELIX 8 AA8 LYS B 79 LEU B 83 5 5 HELIX 9 AA9 SER B 121 SER B 127 1 7 HELIX 10 AB1 LYS B 183 ARG B 188 1 6 HELIX 11 AB2 ILE C 28 HIS C 32 5 5 HELIX 12 AB3 GLU C 61 LYS C 64 5 4 HELIX 13 AB4 LYS C 73 SER C 75 5 3 HELIX 14 AB5 THR C 83 SER C 87 5 5 HELIX 15 AB6 SER C 156 SER C 158 5 3 HELIX 16 AB7 SER C 186 TRP C 188 5 3 HELIX 17 AB8 PRO C 200 SER C 203 5 4 HELIX 18 AB9 LYS D 79 LEU D 83 5 5 HELIX 19 AC1 SER D 121 SER D 127 1 7 HELIX 20 AC2 LYS D 183 ARG D 188 1 6 SHEET 1 AA1 4 GLN A 3 GLN A 6 0 SHEET 2 AA1 4 VAL A 18 SER A 25 -1 O LYS A 23 N GLN A 5 SHEET 3 AA1 4 THR A 77 LEU A 82 -1 O MET A 80 N ILE A 20 SHEET 4 AA1 4 ALA A 67 ASP A 72 -1 N ASP A 72 O THR A 77 SHEET 1 AA2 6 GLU A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 107 VAL A 111 1 O THR A 108 N GLU A 10 SHEET 3 AA2 6 ALA A 88 ARG A 94 -1 N ALA A 88 O LEU A 109 SHEET 4 AA2 6 ILE A 34 ARG A 39 -1 N ARG A 39 O VAL A 89 SHEET 5 AA2 6 LEU A 45 SER A 52 -1 O ILE A 51 N ILE A 34 SHEET 6 AA2 6 ASP A 56A TYR A 59 -1 O ASP A 56A N SER A 52 SHEET 1 AA3 4 GLU A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 107 VAL A 111 1 O THR A 108 N GLU A 10 SHEET 3 AA3 4 ALA A 88 ARG A 94 -1 N ALA A 88 O LEU A 109 SHEET 4 AA3 4 TYR A 102 TRP A 103 -1 O TYR A 102 N ARG A 94 SHEET 1 AA4 4 SER A 120 LEU A 124 0 SHEET 2 AA4 4 MET A 135 TYR A 145 -1 O GLY A 139 N LEU A 124 SHEET 3 AA4 4 LEU A 174 PRO A 184 -1 O LEU A 177 N VAL A 142 SHEET 4 AA4 4 VAL A 163 THR A 165 -1 N HIS A 164 O SER A 180 SHEET 1 AA5 4 SER A 120 LEU A 124 0 SHEET 2 AA5 4 MET A 135 TYR A 145 -1 O GLY A 139 N LEU A 124 SHEET 3 AA5 4 LEU A 174 PRO A 184 -1 O LEU A 177 N VAL A 142 SHEET 4 AA5 4 VAL A 169 GLN A 171 -1 N GLN A 171 O LEU A 174 SHEET 1 AA6 3 THR A 151 TRP A 154 0 SHEET 2 AA6 3 THR A 194 HIS A 199 -1 O ASN A 196 N THR A 153 SHEET 3 AA6 3 THR A 204 LYS A 209 -1 O VAL A 206 N VAL A 197 SHEET 1 AA7 4 MET B 4 SER B 7 0 SHEET 2 AA7 4 VAL B 19 SER B 25 -1 O LYS B 24 N SER B 5 SHEET 3 AA7 4 ASP B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA7 4 PHE B 62 SER B 67 -1 N THR B 63 O THR B 74 SHEET 1 AA8 6 SER B 10 VAL B 13 0 SHEET 2 AA8 6 THR B 102 ARG B 106 1 O GLU B 105 N VAL B 13 SHEET 3 AA8 6 VAL B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA8 6 LEU B 33 GLN B 38 -1 N ALA B 34 O GLN B 89 SHEET 5 AA8 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AA8 6 THR B 53 ARG B 54 -1 O THR B 53 N TYR B 49 SHEET 1 AA9 4 SER B 10 VAL B 13 0 SHEET 2 AA9 4 THR B 102 ARG B 106 1 O GLU B 105 N VAL B 13 SHEET 3 AA9 4 VAL B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA9 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AB1 4 THR B 114 PHE B 118 0 SHEET 2 AB1 4 GLY B 129 PHE B 139 -1 O ASN B 137 N THR B 114 SHEET 3 AB1 4 TYR B 173 THR B 182 -1 O MET B 175 N LEU B 136 SHEET 4 AB1 4 VAL B 159 TRP B 163 -1 N LEU B 160 O THR B 178 SHEET 1 AB2 4 SER B 153 ARG B 155 0 SHEET 2 AB2 4 ASN B 145 ILE B 150 -1 N ILE B 150 O SER B 153 SHEET 3 AB2 4 SER B 191 THR B 197 -1 O GLU B 195 N LYS B 147 SHEET 4 AB2 4 ILE B 205 ASN B 210 -1 O LYS B 207 N CYS B 194 SHEET 1 AB3 4 GLN C 3 GLN C 6 0 SHEET 2 AB3 4 VAL C 18 SER C 25 -1 O LYS C 23 N GLN C 5 SHEET 3 AB3 4 THR C 77 LEU C 82 -1 O MET C 80 N ILE C 20 SHEET 4 AB3 4 ALA C 67 ASP C 72 -1 N ASP C 72 O THR C 77 SHEET 1 AB4 6 GLU C 10 VAL C 12 0 SHEET 2 AB4 6 THR C 107 VAL C 111 1 O THR C 108 N GLU C 10 SHEET 3 AB4 6 ALA C 88 ARG C 94 -1 N ALA C 88 O LEU C 109 SHEET 4 AB4 6 ILE C 34 ARG C 39 -1 N ARG C 39 O VAL C 89 SHEET 5 AB4 6 LEU C 45 SER C 52 -1 O GLU C 46 N LYS C 38 SHEET 6 AB4 6 ASP C 56A TYR C 59 -1 O ASP C 56A N SER C 52 SHEET 1 AB5 4 GLU C 10 VAL C 12 0 SHEET 2 AB5 4 THR C 107 VAL C 111 1 O THR C 108 N GLU C 10 SHEET 3 AB5 4 ALA C 88 ARG C 94 -1 N ALA C 88 O LEU C 109 SHEET 4 AB5 4 TYR C 102 TRP C 103 -1 O TYR C 102 N ARG C 94 SHEET 1 AB6 4 SER C 120 LEU C 124 0 SHEET 2 AB6 4 MET C 135 TYR C 145 -1 O GLY C 139 N LEU C 124 SHEET 3 AB6 4 LEU C 174 PRO C 184 -1 O LEU C 177 N VAL C 142 SHEET 4 AB6 4 VAL C 163 THR C 165 -1 N HIS C 164 O SER C 180 SHEET 1 AB7 4 SER C 120 LEU C 124 0 SHEET 2 AB7 4 MET C 135 TYR C 145 -1 O GLY C 139 N LEU C 124 SHEET 3 AB7 4 LEU C 174 PRO C 184 -1 O LEU C 177 N VAL C 142 SHEET 4 AB7 4 VAL C 169 GLN C 171 -1 N GLN C 171 O LEU C 174 SHEET 1 AB8 3 THR C 151 TRP C 154 0 SHEET 2 AB8 3 THR C 194 HIS C 199 -1 O ASN C 196 N THR C 153 SHEET 3 AB8 3 THR C 204 LYS C 209 -1 O VAL C 206 N VAL C 197 SHEET 1 AB9 4 MET D 4 SER D 7 0 SHEET 2 AB9 4 VAL D 19 SER D 25 -1 O LYS D 24 N SER D 5 SHEET 3 AB9 4 ASP D 70 ILE D 75 -1 O ILE D 75 N VAL D 19 SHEET 4 AB9 4 PHE D 62 SER D 67 -1 N THR D 63 O THR D 74 SHEET 1 AC1 6 SER D 10 VAL D 13 0 SHEET 2 AC1 6 THR D 102 ARG D 106 1 O GLU D 105 N VAL D 13 SHEET 3 AC1 6 VAL D 85 GLN D 90 -1 N TYR D 86 O THR D 102 SHEET 4 AC1 6 LEU D 33 GLN D 38 -1 N TYR D 36 O TYR D 87 SHEET 5 AC1 6 LYS D 45 TYR D 49 -1 O LEU D 47 N TRP D 35 SHEET 6 AC1 6 THR D 53 ARG D 54 -1 O THR D 53 N TYR D 49 SHEET 1 AC2 4 SER D 10 VAL D 13 0 SHEET 2 AC2 4 THR D 102 ARG D 106 1 O GLU D 105 N VAL D 13 SHEET 3 AC2 4 VAL D 85 GLN D 90 -1 N TYR D 86 O THR D 102 SHEET 4 AC2 4 THR D 97 PHE D 98 -1 O THR D 97 N GLN D 90 SHEET 1 AC3 4 THR D 114 PHE D 118 0 SHEET 2 AC3 4 GLY D 129 PHE D 139 -1 O ASN D 137 N THR D 114 SHEET 3 AC3 4 TYR D 173 THR D 182 -1 O MET D 175 N LEU D 136 SHEET 4 AC3 4 VAL D 159 TRP D 163 -1 N LEU D 160 O THR D 178 SHEET 1 AC4 4 SER D 153 ARG D 155 0 SHEET 2 AC4 4 ASN D 145 ILE D 150 -1 N ILE D 150 O SER D 153 SHEET 3 AC4 4 SER D 191 THR D 197 -1 O GLU D 195 N LYS D 147 SHEET 4 AC4 4 ILE D 205 ASN D 210 -1 O LYS D 207 N CYS D 194 SSBOND 1 CYS A 22 CYS A 92 1555 1555 2.22 SSBOND 2 CYS A 140 CYS A 195 1555 1555 2.25 SSBOND 3 CYS B 23 CYS B 88 1555 1555 2.50 SSBOND 4 CYS B 134 CYS B 194 1555 1555 2.07 SSBOND 5 CYS C 22 CYS C 92 1555 1555 2.20 SSBOND 6 CYS C 140 CYS C 195 1555 1555 2.20 SSBOND 7 CYS D 23 CYS D 88 1555 1555 2.48 SSBOND 8 CYS D 134 CYS D 194 1555 1555 2.15 LINK OG SER M 4 C1 A2G M 101 1555 1555 1.39 LINK OG1 THR M 5 C1 A2G M 102 1555 1555 1.39 LINK C ALA M 9 N NH2 M 10 1555 1555 1.34 LINK OG SER N 4 C1 A2G N 101 1555 1555 1.40 LINK OG1 THR N 5 C1 A2G N 102 1555 1555 1.46 LINK C ALA N 9 N NH2 N 10 1555 1555 1.33 CISPEP 1 PHE A 146 PRO A 147 0 -8.46 CISPEP 2 GLU A 148 PRO A 149 0 -4.31 CISPEP 3 TRP A 188 PRO A 189 0 1.66 CISPEP 4 SER B 7 PRO B 8 0 -8.44 CISPEP 5 TYR B 94 PRO B 95 0 -7.15 CISPEP 6 TYR B 140 PRO B 141 0 2.65 CISPEP 7 PHE C 146 PRO C 147 0 -8.45 CISPEP 8 GLU C 148 PRO C 149 0 -4.49 CISPEP 9 TRP C 188 PRO C 189 0 1.15 CISPEP 10 SER D 7 PRO D 8 0 -5.67 CISPEP 11 TYR D 94 PRO D 95 0 -3.89 CISPEP 12 TYR D 140 PRO D 141 0 2.18 CISPEP 13 ALA M 1 PRO M 2 0 3.55 CISPEP 14 ALA N 1 PRO N 2 0 9.91 CRYST1 67.053 111.546 134.962 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007409 0.00000