HEADER IMMUNE SYSTEM 25-FEB-25 9Q8L TITLE CRYSTAL STRUCTURE OF 21A08AP1-FAB IN COMPLEX WITH HUMAN PD-1 AT 1.85 TITLE 2 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF HUIGG1-FAB; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF HUIGG1-FAB; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: PROTEIN PD-1,HPD-1; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: TRUNCATED TO RESIDUES 24-170 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: PDCD1, PD1; SOURCE 16 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS PD-1, IMMUNE CHECKPOINT, FAB, HUIGG1, 21A08AP1, T-CELLS, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.MURER,L.PETERSEN,N.EGLI,U.SALAZAR,P.NEUBERT,A.ZURBACH,A.RAU, AUTHOR 2 C.STOCKER,A.KATOPODIS,C.HUBER,K.CARR,A.ARDUIN REVDAT 1 13-AUG-25 9Q8L 0 JRNL AUTH P.MURER,L.PETERSEN,N.EGLI,U.SALAZAR,P.NEUBERT,A.ZURBACH, JRNL AUTH 2 A.RAU,C.STOCKER,D.REICHENSTEIN,A.KATOPODIS,C.HUBER JRNL TITL ANV600 IS A NOVEL PD-1 TARGETED IL-2R BETA GAMMA AGONIST JRNL TITL 2 THAT SELECTIVELY EXPANDS TUMOR ANTIGEN-SPECIFIC T CELLS AND JRNL TITL 3 POTENTIATES PD-1 CHECKPOINT INHIBITOR THERAPY. JRNL REF J IMMUNOTHER CANCER V. 13 2025 JRNL REFN ESSN 2051-1426 JRNL PMID 40664449 JRNL DOI 10.1136/JITC-2025-011905 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 61683 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.019 REMARK 3 FREE R VALUE TEST SET COUNT : 3096 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4236 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 115 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10600 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.10300 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4367 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3954 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5984 ; 1.777 ; 1.795 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9173 ; 1.959 ; 1.721 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 7.311 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 22 ;14.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 643 ;12.714 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 705 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5133 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 973 ; 0.015 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 624 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 40 ; 0.344 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2141 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 293 ; 0.175 ; 0.200 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): 2220 ; 2.988 ; 3.164 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2220 ; 2.987 ; 3.165 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2782 ; 3.938 ; 5.656 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2783 ; 3.939 ; 5.658 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2147 ; 4.697 ; 3.747 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2148 ; 4.696 ; 3.747 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3195 ; 6.769 ; 6.639 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3196 ; 6.768 ; 6.640 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9Q8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292144834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9655 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 81.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 1.52300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 25% W/V PEG 3,350, REMARK 280 20% W/V MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 30.91950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.84200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.12050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.84200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.91950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.12050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: H, L, A, B, C 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 ARG L 1 REMARK 465 PHE A 24 REMARK 465 LEU A 25 REMARK 465 ASP A 26 REMARK 465 SER A 27 REMARK 465 PRO A 28 REMARK 465 ASP A 29 REMARK 465 ASP A 85 REMARK 465 ARG A 86 REMARK 465 SER A 87 REMARK 465 GLN A 88 REMARK 465 PRO A 89 REMARK 465 GLY A 90 REMARK 465 GLN A 91 REMARK 465 ALA A 149 REMARK 465 GLU A 150 REMARK 465 VAL A 151 REMARK 465 PRO A 152 REMARK 465 THR A 153 REMARK 465 ALA A 154 REMARK 465 HIS A 155 REMARK 465 PRO A 156 REMARK 465 SER A 157 REMARK 465 PRO A 158 REMARK 465 SER A 159 REMARK 465 PRO A 160 REMARK 465 ARG A 161 REMARK 465 PRO A 162 REMARK 465 ALA A 163 REMARK 465 GLY A 164 REMARK 465 GLN A 165 REMARK 465 PHE A 166 REMARK 465 GLN A 167 REMARK 465 THR A 168 REMARK 465 LEU A 169 REMARK 465 VAL A 170 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU H 1 CG CD OE1 OE2 REMARK 470 LYS H 65 CD CE NZ REMARK 470 ARG H 87 CD NE CZ NH1 NH2 REMARK 470 LYS L 46 CD CE NZ REMARK 470 LYS L 160 CG CD CE NZ REMARK 470 GLU L 214 CG CD OE1 OE2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 ASP A 92 CG OD1 OD2 REMARK 470 ARG A 96 CG CD NE CZ NH1 NH2 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 L 55 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG L 62 CD - NE - CZ ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG L 62 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG L 62 NE - CZ - NH2 ANGL. DEV. = -6.9 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 GLU H 99 166.58 74.51 REMARK 500 ASP H 146 62.71 61.65 REMARK 500 ASN L 28 -96.38 -121.19 REMARK 500 ASN L 52 -42.97 74.78 REMARK 500 ASN L 53 13.21 -151.98 REMARK 500 ASP L 155 63.82 32.46 REMARK 500 SER L 156 -16.32 79.19 REMARK 500 ASN L 174 -2.87 80.36 REMARK 500 ARG A 104 -49.73 -150.29 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 L 17 0.07 SIDE CHAIN REMARK 500 ARG L 62 0.16 SIDE CHAIN REMARK 500 ARG L 80 0.09 SIDE CHAIN REMARK 500 ARG A 143 0.08 SIDE CHAIN REMARK 500 ARG A 147 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9Q8L H 1 218 PDB 9Q8L 9Q8L 1 218 DBREF 9Q8L L 1 216 PDB 9Q8L 9Q8L 1 216 DBREF 9Q8L A 24 170 UNP Q15116 PDCD1_HUMAN 24 170 SEQRES 1 H 218 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 218 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 218 PHE THR PHE SER ILE ASN ALA MET THR TRP VAL ARG GLN SEQRES 4 H 218 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER THR ILE SER SEQRES 5 H 218 GLY SER GLY PHE SER THR TYR TYR ALA ASP SER LEU LYS SEQRES 6 H 218 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 218 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 218 ALA VAL TYR TYR CYS ALA LYS GLU VAL TYR GLY ASP TYR SEQRES 9 H 218 TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SER SEQRES 10 H 218 THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER SEQRES 11 H 218 LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU SEQRES 12 H 218 VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP SEQRES 13 H 218 ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO SEQRES 14 H 218 ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER SEQRES 15 H 218 VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR SEQRES 16 H 218 TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS SEQRES 17 H 218 VAL ASP LYS ARG VAL GLU PRO LYS SER CYS SEQRES 1 L 216 ARG SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 L 216 PRO GLY GLN ARG VAL SER ILE SER CYS SER GLY ALA SER SEQRES 3 L 216 SER ASN ILE GLY SER GLN SER VAL PHE TRP TYR GLN GLN SEQRES 4 L 216 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR SER ASN SEQRES 5 L 216 ASN GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 L 216 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 L 216 LEU ARG SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA SEQRES 8 L 216 TRP ASP ASP SER LEU SER ILE TRP VAL PHE GLY GLY GLY SEQRES 9 L 216 THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 L 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 L 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 L 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 L 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 L 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 L 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 L 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 L 216 THR VAL ALA PRO THR GLU CYS SER SEQRES 1 A 147 PHE LEU ASP SER PRO ASP ARG PRO TRP ASN PRO PRO THR SEQRES 2 A 147 PHE SER PRO ALA LEU LEU VAL VAL THR GLU GLY ASP ASN SEQRES 3 A 147 ALA THR PHE THR CYS SER PHE SER ASN THR SER GLU SER SEQRES 4 A 147 PHE VAL LEU ASN TRP TYR ARG MET SER PRO SER ASN GLN SEQRES 5 A 147 THR ASP LYS LEU ALA ALA PHE PRO GLU ASP ARG SER GLN SEQRES 6 A 147 PRO GLY GLN ASP CYS ARG PHE ARG VAL THR GLN LEU PRO SEQRES 7 A 147 ASN GLY ARG ASP PHE HIS MET SER VAL VAL ARG ALA ARG SEQRES 8 A 147 ARG ASN ASP SER GLY THR TYR LEU CYS GLY ALA ILE SER SEQRES 9 A 147 LEU ALA PRO LYS ALA GLN ILE LYS GLU SER LEU ARG ALA SEQRES 10 A 147 GLU LEU ARG VAL THR GLU ARG ARG ALA GLU VAL PRO THR SEQRES 11 A 147 ALA HIS PRO SER PRO SER PRO ARG PRO ALA GLY GLN PHE SEQRES 12 A 147 GLN THR LEU VAL HET NAG B 1 14 HET NAG B 2 14 HET FUC B 3 10 HET NAG C 1 14 HET NAG C 2 14 HET FUC C 3 10 HET EDO H 301 4 HET EDO H 302 4 HET EDO H 303 4 HET DMS H 304 4 HET PO4 L 301 5 HET EDO L 302 4 HET NAG A 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM PO4 PHOSPHATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 NAG 5(C8 H15 N O6) FORMUL 4 FUC 2(C6 H12 O5) FORMUL 6 EDO 4(C2 H6 O2) FORMUL 9 DMS C2 H6 O S FORMUL 10 PO4 O4 P 3- FORMUL 13 HOH *343(H2 O) HELIX 1 AA1 THR H 28 ASN H 32 5 5 HELIX 2 AA2 ASP H 62 LYS H 65 5 4 HELIX 3 AA3 ASN H 74 LYS H 76 5 3 HELIX 4 AA4 ARG H 87 THR H 91 5 5 HELIX 5 AA5 SER H 129 LYS H 131 5 3 HELIX 6 AA6 SER H 158 ALA H 160 5 3 HELIX 7 AA7 SER H 189 LEU H 191 5 3 HELIX 8 AA8 LYS H 203 ASN H 206 5 4 HELIX 9 AA9 ARG L 80 GLU L 84 5 5 HELIX 10 AB1 SER L 125 ALA L 131 1 7 HELIX 11 AB2 THR L 185 HIS L 192 1 8 HELIX 12 AB3 ARG A 114 SER A 118 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O ALA H 23 N LEU H 5 SHEET 3 AA1 4 THR H 78 MET H 83 -1 O LEU H 81 N LEU H 20 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 109 VAL H 113 1 O THR H 112 N GLY H 10 SHEET 3 AA2 6 ALA H 92 LYS H 98 -1 N TYR H 94 O THR H 109 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 58 TYR H 60 -1 O TYR H 59 N THR H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 109 VAL H 113 1 O THR H 112 N GLY H 10 SHEET 3 AA3 4 ALA H 92 LYS H 98 -1 N TYR H 94 O THR H 109 SHEET 4 AA3 4 TYR H 104 TRP H 105 -1 O TYR H 104 N LYS H 98 SHEET 1 AA4 4 SER H 122 LEU H 126 0 SHEET 2 AA4 4 THR H 137 TYR H 147 -1 O LYS H 145 N SER H 122 SHEET 3 AA4 4 TYR H 178 PRO H 187 -1 O LEU H 180 N VAL H 144 SHEET 4 AA4 4 VAL H 165 THR H 167 -1 N HIS H 166 O VAL H 183 SHEET 1 AA5 4 THR H 133 SER H 134 0 SHEET 2 AA5 4 THR H 137 TYR H 147 -1 O THR H 137 N SER H 134 SHEET 3 AA5 4 TYR H 178 PRO H 187 -1 O LEU H 180 N VAL H 144 SHEET 4 AA5 4 VAL H 171 LEU H 172 -1 N VAL H 171 O SER H 179 SHEET 1 AA6 3 THR H 153 TRP H 156 0 SHEET 2 AA6 3 ILE H 197 HIS H 202 -1 O ASN H 199 N SER H 155 SHEET 3 AA6 3 THR H 207 ARG H 212 -1 O VAL H 209 N VAL H 200 SHEET 1 AA7 5 SER L 9 GLY L 12 0 SHEET 2 AA7 5 THR L 105 VAL L 109 1 O THR L 108 N ALA L 10 SHEET 3 AA7 5 ALA L 85 ASP L 93 -1 N ALA L 85 O LEU L 107 SHEET 4 AA7 5 PHE L 35 GLN L 39 -1 N GLN L 39 O ASP L 86 SHEET 5 AA7 5 LYS L 46 ILE L 49 -1 O LEU L 48 N TRP L 36 SHEET 1 AA8 4 SER L 9 GLY L 12 0 SHEET 2 AA8 4 THR L 105 VAL L 109 1 O THR L 108 N ALA L 10 SHEET 3 AA8 4 ALA L 85 ASP L 93 -1 N ALA L 85 O LEU L 107 SHEET 4 AA8 4 ILE L 98 PHE L 101 -1 O ILE L 98 N ASP L 93 SHEET 1 AA9 3 VAL L 18 SER L 23 0 SHEET 2 AA9 3 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 3 AA9 3 PHE L 63 SER L 68 -1 N SER L 64 O ALA L 75 SHEET 1 AB1 4 SER L 118 PHE L 122 0 SHEET 2 AB1 4 ALA L 134 PHE L 143 -1 O VAL L 137 N PHE L 122 SHEET 3 AB1 4 TYR L 176 LEU L 184 -1 O ALA L 178 N ILE L 140 SHEET 4 AB1 4 VAL L 163 THR L 165 -1 N GLU L 164 O TYR L 181 SHEET 1 AB2 4 SER L 118 PHE L 122 0 SHEET 2 AB2 4 ALA L 134 PHE L 143 -1 O VAL L 137 N PHE L 122 SHEET 3 AB2 4 TYR L 176 LEU L 184 -1 O ALA L 178 N ILE L 140 SHEET 4 AB2 4 SER L 169 LYS L 170 -1 N SER L 169 O ALA L 177 SHEET 1 AB3 4 SER L 157 VAL L 159 0 SHEET 2 AB3 4 THR L 149 ALA L 154 -1 N ALA L 154 O SER L 157 SHEET 3 AB3 4 TYR L 195 HIS L 201 -1 O GLN L 198 N ALA L 151 SHEET 4 AB3 4 SER L 204 VAL L 210 -1 O SER L 204 N HIS L 201 SHEET 1 AB4 4 THR A 36 SER A 38 0 SHEET 2 AB4 4 ALA A 50 SER A 55 -1 O THR A 53 N SER A 38 SHEET 3 AB4 4 ASP A 105 VAL A 110 -1 O VAL A 110 N ALA A 50 SHEET 4 AB4 4 PHE A 95 GLN A 99 -1 N THR A 98 O HIS A 107 SHEET 1 AB5 5 LEU A 41 THR A 45 0 SHEET 2 AB5 5 ALA A 140 THR A 145 1 O THR A 145 N VAL A 44 SHEET 3 AB5 5 GLY A 119 SER A 127 -1 N TYR A 121 O ALA A 140 SHEET 4 AB5 5 PHE A 63 MET A 70 -1 N ASN A 66 O GLY A 124 SHEET 5 AB5 5 THR A 76 PHE A 82 -1 O ASP A 77 N ARG A 69 SHEET 1 AB6 4 LEU A 41 THR A 45 0 SHEET 2 AB6 4 ALA A 140 THR A 145 1 O THR A 145 N VAL A 44 SHEET 3 AB6 4 GLY A 119 SER A 127 -1 N TYR A 121 O ALA A 140 SHEET 4 AB6 4 GLN A 133 GLU A 136 -1 O LYS A 135 N ALA A 125 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.05 SSBOND 2 CYS H 142 CYS H 198 1555 1555 2.01 SSBOND 3 CYS H 218 CYS L 215 1555 1555 2.06 SSBOND 4 CYS L 22 CYS L 89 1555 1555 2.09 SSBOND 5 CYS L 138 CYS L 197 1555 1555 2.06 SSBOND 6 CYS A 54 CYS A 123 1555 1555 2.06 LINK ND2 ASN A 49 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 58 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 116 C1 NAG A 201 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.39 LINK O6 NAG B 1 C1 FUC B 3 1555 1555 1.40 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.40 CISPEP 1 PHE H 148 PRO H 149 0 -7.72 CISPEP 2 GLU H 150 PRO H 151 0 -1.74 CISPEP 3 TYR L 144 PRO L 145 0 3.68 CISPEP 4 SER A 38 PRO A 39 0 -4.56 CISPEP 5 SER A 38 PRO A 39 0 0.58 CISPEP 6 PHE A 82 PRO A 83 0 -4.74 CISPEP 7 ALA A 129 PRO A 130 0 5.69 CRYST1 61.839 70.241 163.684 90.00 90.00 90.00 P 21 21 21 4 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 0.016171 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006109 0.00000