HEADER IMMUNE SYSTEM 30-SEP-24 9GXH TITLE NANOBODY BOUND TO TBA G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THROMBIN-BINDING APTAMER (TBA); COMPND 7 CHAIN: C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, DNA, THROMBIN, NANOBODY, THROMBIN-BINDING APTAMER, TBA, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.HADZI,M.PEVEC REVDAT 1 11-JUN-25 9GXH 0 JRNL AUTH M.PEVEC,T.MEDVED,M.KOVACIC,N.ZERJAV,J.IMPERL,J.PLAVEC,J.LAH, JRNL AUTH 2 R.LORIS,S.HADZI JRNL TITL STRUCTURAL BASIS OF G-QUADRUPLEX RECOGNITION BY A CAMELID JRNL TITL 2 ANTIBODY FRAGMENT. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40433978 JRNL DOI 10.1093/NAR/GKAF453 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 23145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.640 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.3320 - 4.5779 1.00 1578 150 0.1502 0.1624 REMARK 3 2 4.5779 - 3.6341 0.95 1481 140 0.1191 0.1465 REMARK 3 3 3.6341 - 3.1748 0.90 1408 133 0.1310 0.1619 REMARK 3 4 3.1748 - 2.8846 1.00 1542 146 0.1649 0.1939 REMARK 3 5 2.8846 - 2.6779 1.00 1527 145 0.1596 0.2155 REMARK 3 6 2.6779 - 2.5200 0.87 1347 127 0.1746 0.2395 REMARK 3 7 2.5200 - 2.3938 1.00 1534 144 0.1751 0.2504 REMARK 3 8 2.3938 - 2.2896 1.00 1529 145 0.1639 0.2337 REMARK 3 9 2.2896 - 2.2015 1.00 1553 147 0.1713 0.2498 REMARK 3 10 2.2015 - 2.1255 1.00 1517 143 0.1619 0.2356 REMARK 3 11 2.1255 - 2.0591 1.00 1543 146 0.1673 0.2380 REMARK 3 12 2.0591 - 2.0002 1.00 1511 144 0.1593 0.2016 REMARK 3 13 2.0002 - 1.9475 1.00 1562 147 0.1674 0.2205 REMARK 3 14 1.9475 - 1.9000 1.00 1513 143 0.1732 0.2238 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2567 REMARK 3 ANGLE : 0.973 3615 REMARK 3 CHIRALITY : 0.055 392 REMARK 3 PLANARITY : 0.005 350 REMARK 3 DIHEDRAL : 20.823 1387 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 115) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8192 -3.7155 24.4925 REMARK 3 T TENSOR REMARK 3 T11: 0.0511 T22: 0.0631 REMARK 3 T33: 0.0488 T12: 0.0058 REMARK 3 T13: 0.0011 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.7476 L22: 1.1082 REMARK 3 L33: 1.1019 L12: 0.3637 REMARK 3 L13: 0.0394 L23: -0.0038 REMARK 3 S TENSOR REMARK 3 S11: -0.0572 S12: 0.0881 S13: -0.0249 REMARK 3 S21: -0.0315 S22: 0.0406 S23: -0.0425 REMARK 3 S31: 0.0270 S32: 0.0231 S33: 0.0198 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 3 THROUGH 115) REMARK 3 ORIGIN FOR THE GROUP (A): 26.8195 18.4601 10.7345 REMARK 3 T TENSOR REMARK 3 T11: 0.1136 T22: 0.1240 REMARK 3 T33: 0.0714 T12: -0.0410 REMARK 3 T13: -0.0001 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.4601 L22: 1.8710 REMARK 3 L33: 2.2112 L12: -0.3470 REMARK 3 L13: -0.5353 L23: 0.1992 REMARK 3 S TENSOR REMARK 3 S11: -0.0708 S12: -0.0042 S13: 0.0348 REMARK 3 S21: -0.0578 S22: 0.1047 S23: -0.1500 REMARK 3 S31: -0.1240 S32: 0.1783 S33: 0.0091 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 21.1161 19.2805 27.5851 REMARK 3 T TENSOR REMARK 3 T11: 0.0740 T22: 0.0776 REMARK 3 T33: 0.0463 T12: 0.0024 REMARK 3 T13: -0.0022 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.0485 L22: 3.6014 REMARK 3 L33: 2.4986 L12: 0.5908 REMARK 3 L13: -0.1137 L23: 1.7507 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.0006 S13: 0.0778 REMARK 3 S21: -0.0328 S22: 0.0777 S23: 0.1173 REMARK 3 S31: -0.0768 S32: 0.0536 S33: -0.0425 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3221 25.4863 -7.2336 REMARK 3 T TENSOR REMARK 3 T11: 0.1574 T22: 0.1650 REMARK 3 T33: 0.0792 T12: -0.0305 REMARK 3 T13: -0.0146 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.7125 L22: 3.6621 REMARK 3 L33: 2.6454 L12: -1.0671 REMARK 3 L13: 0.0117 L23: -0.5558 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: -0.0624 S13: 0.0767 REMARK 3 S21: 0.4189 S22: 0.0278 S23: -0.1416 REMARK 3 S31: -0.1077 S32: 0.3179 S33: -0.0078 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9GXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292142137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO ANISOTROPY CORRECTION REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43889 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 70.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 3.64900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 40.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M REMARK 280 PHOSPHATE/CITRATE, PH = 4.2, 20 % W/V PEG 8000 CRYOSOAK: SAME REMARK 280 SOLUTION WITH 30% GLYCEROL, PH 4.2, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.66550 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 36.28400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -29.66550 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 GLN B 1 REMARK 465 VAL B 2 REMARK 465 GLY B 26 REMARK 465 SER B 27 REMARK 465 ARG B 28 REMARK 465 PHE B 29 REMARK 465 SER B 30 REMARK 465 SER B 31 REMARK 465 HIS B 116 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 REMARK 465 HIS B 120 REMARK 465 HIS B 121 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 GLN A 1 CG CD OE1 NE2 REMARK 470 HIS A 116 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 ASN B 73 CG OD1 ND2 REMARK 470 ARG B 98 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 99 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 400 O HOH A 419 2.02 REMARK 500 O HOH A 365 O HOH A 414 2.08 REMARK 500 O HOH B 264 O HOH C 220 2.11 REMARK 500 NH1 ARG A 58 O ARG B 45 2.12 REMARK 500 O HOH A 410 O HOH A 415 2.13 REMARK 500 O HOH B 252 O HOH C 223 2.17 REMARK 500 OP1 DT C 12 O HOH C 201 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 428 O HOH A 440 1655 2.12 REMARK 500 OH TYR A 37 OP2 DT C 13 2645 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 8 O3' DG D 8 C3' -0.040 REMARK 500 REMARK 500 REMARK: NULL 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 DG C 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 15 O4' - C1' - N9 ANGL. DEV. = 2.3 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 30 0.11 -67.87 REMARK 500 LYS B 75 -160.10 -118.73 REMARK 500 ASN B 76 58.98 -114.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 363 O REMARK 620 2 HOH A 395 O 57.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 1 O6 REMARK 620 2 DG C 1 O6 1.6 REMARK 620 3 DG C 2 O6 63.0 63.7 REMARK 620 4 DG C 5 O6 119.8 121.3 72.5 REMARK 620 5 DG C 6 O6 78.2 79.3 97.6 69.5 REMARK 620 6 DG C 10 O6 119.8 119.5 165.3 95.1 70.1 REMARK 620 7 DG C 11 O6 165.6 164.4 112.0 68.1 116.3 68.8 REMARK 620 8 DG C 14 O6 93.2 92.4 64.9 102.8 162.5 127.1 72.7 REMARK 620 9 DG C 15 O6 77.7 76.2 117.9 162.3 119.9 76.1 94.3 72.1 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 1 O6 REMARK 620 2 DG D 1 O6 14.1 REMARK 620 3 DG D 2 O6 66.4 60.5 REMARK 620 4 DG D 5 O6 116.3 121.2 70.8 REMARK 620 5 DG D 6 O6 70.0 83.8 95.8 69.9 REMARK 620 6 DG D 10 O6 112.5 121.4 167.4 100.0 72.6 REMARK 620 7 DG D 11 O6 172.8 160.0 115.2 70.3 116.1 67.6 REMARK 620 8 DG D 14 O6 100.3 86.3 66.2 103.0 162.0 125.4 74.7 REMARK 620 9 DG D 15 O6 77.2 71.4 115.7 166.4 119.4 75.2 96.1 71.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9GV4 RELATED DB: PDB REMARK 900 NANOBODY IN FREE FORM DBREF 9GXH A 1 121 PDB 9GXH 9GXH 1 121 DBREF 9GXH B 1 121 PDB 9GXH 9GXH 1 121 DBREF 9GXH C 1 15 PDB 9GXH 9GXH 1 15 DBREF 9GXH D 1 15 PDB 9GXH 9GXH 1 15 SEQRES 1 A 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 121 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 121 SER ARG PHE SER SER ASN THR MET THR TRP TYR ARG GLN SEQRES 4 A 121 ALA PRO GLY LYS GLN ARG GLU TRP VAL ALA THR MET ARG SEQRES 5 A 121 SER ILE GLY THR THR ARG TYR ALA SER SER VAL GLU GLY SEQRES 6 A 121 ARG PHE THR LEU SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 A 121 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 A 121 VAL TYR TYR CYS ASN LEU ARG ARG GLY GLY GLY ILE TYR SEQRES 9 A 121 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 10 A 121 HIS HIS HIS HIS SEQRES 1 B 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 121 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 121 SER ARG PHE SER SER ASN THR MET THR TRP TYR ARG GLN SEQRES 4 B 121 ALA PRO GLY LYS GLN ARG GLU TRP VAL ALA THR MET ARG SEQRES 5 B 121 SER ILE GLY THR THR ARG TYR ALA SER SER VAL GLU GLY SEQRES 6 B 121 ARG PHE THR LEU SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 121 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 121 VAL TYR TYR CYS ASN LEU ARG ARG GLY GLY GLY ILE TYR SEQRES 9 B 121 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 10 B 121 HIS HIS HIS HIS SEQRES 1 C 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 C 15 DG DG SEQRES 1 D 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 D 15 DG DG HET K A 201 1 HET EDO A 202 4 HET K C 101 1 HET K D 101 1 HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 K 3(K 1+) FORMUL 6 EDO C2 H6 O2 FORMUL 9 HOH *345(H2 O) HELIX 1 AA1 ARG A 28 ASN A 32 5 5 HELIX 2 AA2 LYS A 86 THR A 90 5 5 HELIX 3 AA3 LYS B 86 THR B 90 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O ALA A 23 N GLN A 5 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 109 SER A 114 1 O SER A 114 N VAL A 12 SHEET 3 AA2 6 ALA A 91 ARG A 99 -1 N TYR A 93 O THR A 109 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N TYR A 37 O TYR A 94 SHEET 5 AA2 6 GLU A 46 MET A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O ARG A 58 N THR A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 109 SER A 114 1 O SER A 114 N VAL A 12 SHEET 3 AA3 4 ALA A 91 ARG A 99 -1 N TYR A 93 O THR A 109 SHEET 4 AA3 4 GLY A 102 TRP A 105 -1 O TYR A 104 N LEU A 97 SHEET 1 AA4 4 LEU B 4 SER B 7 0 SHEET 2 AA4 4 LEU B 18 ALA B 24 -1 O SER B 21 N SER B 7 SHEET 3 AA4 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 18 SHEET 4 AA4 4 PHE B 67 ARG B 71 -1 N SER B 70 O TYR B 79 SHEET 1 AA5 6 GLY B 10 GLN B 13 0 SHEET 2 AA5 6 THR B 109 SER B 114 1 O THR B 112 N GLY B 10 SHEET 3 AA5 6 ALA B 91 ARG B 99 -1 N TYR B 93 O THR B 109 SHEET 4 AA5 6 THR B 33 GLN B 39 -1 N TYR B 37 O TYR B 94 SHEET 5 AA5 6 GLU B 46 MET B 51 -1 O ALA B 49 N TRP B 36 SHEET 6 AA5 6 THR B 57 TYR B 59 -1 O ARG B 58 N THR B 50 SHEET 1 AA6 4 GLY B 10 GLN B 13 0 SHEET 2 AA6 4 THR B 109 SER B 114 1 O THR B 112 N GLY B 10 SHEET 3 AA6 4 ALA B 91 ARG B 99 -1 N TYR B 93 O THR B 109 SHEET 4 AA6 4 GLY B 102 TRP B 105 -1 O TYR B 104 N LEU B 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.06 SSBOND 2 CYS B 22 CYS B 95 1555 1555 2.06 LINK K K A 201 O HOH A 363 1555 1555 3.21 LINK K K A 201 O HOH A 395 1555 1555 3.39 LINK O6 A DG C 1 K K C 101 1555 1555 2.63 LINK O6 B DG C 1 K K C 101 1555 1555 2.66 LINK O6 DG C 2 K K C 101 1555 1555 2.92 LINK O6 DG C 5 K K C 101 1555 1555 2.71 LINK O6 DG C 6 K K C 101 1555 1555 2.74 LINK O6 DG C 10 K K C 101 1555 1555 2.76 LINK O6 DG C 11 K K C 101 1555 1555 2.81 LINK O6 DG C 14 K K C 101 1555 1555 2.83 LINK O6 DG C 15 K K C 101 1555 1555 2.65 LINK O6 A DG D 1 K K D 101 1555 1555 2.64 LINK O6 B DG D 1 K K D 101 1555 1555 2.74 LINK O6 DG D 2 K K D 101 1555 1555 3.01 LINK O6 DG D 5 K K D 101 1555 1555 2.74 LINK O6 DG D 6 K K D 101 1555 1555 2.78 LINK O6 DG D 10 K K D 101 1555 1555 2.69 LINK O6 DG D 11 K K D 101 1555 1555 2.70 LINK O6 DG D 14 K K D 101 1555 1555 2.85 LINK O6 DG D 15 K K D 101 1555 1555 2.68 CRYST1 36.284 59.331 70.625 90.00 95.79 90.00 P 1 21 1 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 0.027560 0.000000 0.002795 0.00000 SCALE2 0.000000 0.016855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014232 0.00000