HEADER IMMUNE SYSTEM 16-JAN-20 6VJN TITLE STRUCTURE OF NHP D11A.B5FAB IN COMPLEX WITH 16055 V2B PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D11A.B5 FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: D11A.B5 FAB LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: V2B PEPTIDE; COMPND 11 CHAIN: G, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606 KEYWDS FRAGMENT BINDING ANTIGEN AND PEPTIDE COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.SINGH,T.J.LIBAN,M.PANCERA REVDAT 3 11-OCT-23 6VJN 1 REMARK REVDAT 2 02-FEB-22 6VJN 1 JRNL REMARK REVDAT 1 20-JAN-21 6VJN 0 JRNL AUTH S.S.ALJEDANI,T.J.LIBAN,K.TRAN,G.PHAD,S.SINGH,V.DUBROVSKAYA, JRNL AUTH 2 P.PUSHPARAJ,P.MARTINEZ-MURILLO,J.RODARTE,A.MILEANT, JRNL AUTH 3 V.MANGALA PRASAD,R.KINZELMAN,S.O'DELL,J.R.MASCOLA,K.K.LEE, JRNL AUTH 4 G.B.KARLSSON HEDESTAM,R.T.WYATT,M.PANCERA JRNL TITL STRUCTURALLY RELATED BUT GENETICALLY UNRELATED ANTIBODY JRNL TITL 2 LINEAGES CONVERGE ON AN IMMUNODOMINANT HIV-1 ENV JRNL TITL 3 NEUTRALIZING DETERMINANT FOLLOWING TRIMER IMMUNIZATION. JRNL REF PLOS PATHOG. V. 17 09543 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 34559844 JRNL DOI 10.1371/JOURNAL.PPAT.1009543 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 33780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1707 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 41.9800 - 4.5800 1.00 2863 152 0.1634 0.2069 REMARK 3 2 4.5800 - 3.6300 1.00 2734 144 0.1494 0.1779 REMARK 3 3 3.6300 - 3.1700 1.00 2712 148 0.1587 0.2409 REMARK 3 4 3.1700 - 2.8800 1.00 2697 136 0.1825 0.2418 REMARK 3 5 2.8800 - 2.6800 1.00 2652 147 0.1881 0.2364 REMARK 3 6 2.6800 - 2.5200 1.00 2681 149 0.2013 0.3099 REMARK 3 7 2.5200 - 2.3900 1.00 2680 136 0.2072 0.2730 REMARK 3 8 2.3900 - 2.2900 1.00 2640 145 0.2035 0.2872 REMARK 3 9 2.2900 - 2.2000 1.00 2648 139 0.2037 0.2935 REMARK 3 10 2.2000 - 2.1300 0.99 2629 153 0.2146 0.2678 REMARK 3 11 2.1300 - 2.0600 0.98 2568 144 0.2345 0.2403 REMARK 3 12 2.0600 - 2.0000 0.96 2569 114 0.2612 0.3290 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.229 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.383 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.14 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 : 0.011 3471 REMARK 3 ANGLE : 1.107 4758 REMARK 3 CHIRALITY : 0.065 548 REMARK 3 PLANARITY : 0.008 607 REMARK 3 DIHEDRAL : 4.440 3031 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 17.6390 -8.0937 -7.4937 REMARK 3 T TENSOR REMARK 3 T11: 0.1377 T22: 0.3272 REMARK 3 T33: 0.1591 T12: -0.0082 REMARK 3 T13: -0.0010 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.6250 L22: 1.2531 REMARK 3 L33: 1.9019 L12: 0.0873 REMARK 3 L13: 0.1192 L23: -0.4209 REMARK 3 S TENSOR REMARK 3 S11: -0.0093 S12: 0.0805 S13: -0.0052 REMARK 3 S21: -0.0007 S22: -0.0062 S23: 0.0146 REMARK 3 S31: -0.2772 S32: -0.0257 S33: 0.0150 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 6VJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246486. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PDB ENTRY 6RCS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.0, 1.32 M REMARK 280 SODIUM/POTASSSIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 32.39000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.72500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.72500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.39000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.39000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, G, F 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 MET H -18 REMARK 465 GLY H -17 REMARK 465 TRP H -16 REMARK 465 SER H -15 REMARK 465 CYS H -14 REMARK 465 ILE H -13 REMARK 465 ILE H -12 REMARK 465 LEU H -11 REMARK 465 PHE H -10 REMARK 465 LEU H -9 REMARK 465 VAL H -8 REMARK 465 ALA H -7 REMARK 465 THR H -6 REMARK 465 ALA H -5 REMARK 465 THR H -4 REMARK 465 GLY H -3 REMARK 465 VAL H -2 REMARK 465 HIS H -1 REMARK 465 SER H 0 REMARK 465 LYS H 132 REMARK 465 SER H 133 REMARK 465 THR H 134 REMARK 465 SER H 135 REMARK 465 GLY H 136 REMARK 465 LYS H 219 REMARK 465 SER H 220 REMARK 465 CYS H 221 REMARK 465 MET L -18 REMARK 465 GLY L -17 REMARK 465 TRP L -16 REMARK 465 SER L -15 REMARK 465 CYS L -14 REMARK 465 ILE L -13 REMARK 465 ILE L -12 REMARK 465 LEU L -11 REMARK 465 PHE L -10 REMARK 465 LEU L -9 REMARK 465 VAL L -8 REMARK 465 ALA L -7 REMARK 465 THR L -6 REMARK 465 ALA L -5 REMARK 465 THR L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 VAL L -1 REMARK 465 THR L 0 REMARK 465 ASP L 151 REMARK 465 THR L 209 REMARK 465 GLU L 210 REMARK 465 CYS L 211 REMARK 465 SER L 212 REMARK 465 ASP F 180 REMARK 465 ILE F 181 REMARK 465 VAL F 182 REMARK 465 PRO F 183 REMARK 465 LEU F 184 REMARK 465 GLU F 185 REMARK 465 GLY F 186D REMARK 465 ASN F 186E REMARK 465 SER F 186F 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 H 3 CD OE1 NE2 REMARK 470 ARG H 101 CG CD NE CZ NH1 NH2 REMARK 470 SER H 130 O OG REMARK 470 SER H 131 OG REMARK 470 THR H 138 OG1 CG2 REMARK 470 GLN H 174 NE2 REMARK 470 THR H 196 OG1 CG2 REMARK 470 ARG H 215 CG CD NE CZ NH1 NH2 REMARK 470 GLU H 217 CG CD OE1 OE2 REMARK 470 GLU L 1 CG CD OE1 OE2 REMARK 470 ASP L 29 OD1 OD2 REMARK 470 SER L 56 OG REMARK 470 ASP L 93 OD1 OD2 REMARK 470 LYS L 110 CD CE NZ REMARK 470 ASN L 128 CG OD1 ND2 REMARK 470 LYS L 129 CE NZ REMARK 470 LYS L 149 CG CD CE NZ REMARK 470 SER L 152 OG REMARK 470 VAL L 155 CG1 CG2 REMARK 470 LYS L 156 CG CD CE NZ REMARK 470 GLU L 160 CG CD OE1 OE2 REMARK 470 GLU L 183 CB CG CD OE1 OE2 REMARK 470 LYS L 186 CG CD CE NZ REMARK 470 ARG L 189 CG CD NE CZ NH1 NH2 REMARK 470 SER L 190 OG REMARK 470 SER L 200 OG REMARK 470 GLU L 203 CG CD OE1 OE2 REMARK 470 LYS L 204 CE NZ REMARK 470 GLU F 186 CD OE1 OE2 REMARK 470 TYR F 191 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG F 192 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER L 14 N CA C O CB OG 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 H 532 O HOH H 549 2.02 REMARK 500 O HOH L 412 O HOH L 501 2.09 REMARK 500 O HOH L 467 O HOH L 480 2.13 REMARK 500 OE2 GLU L 124 OG1 THR L 131 2.19 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 CYS H 92 CB CYS H 92 SG -0.108 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 CYS H 143 CA - CB - SG ANGL. DEV. = 7.7 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 H 15 -16.02 85.52 REMARK 500 ASP H 31 -174.43 61.60 REMARK 500 TYR H 32 -139.63 60.15 REMARK 500 ASP L 51 -50.61 78.44 REMARK 500 ASN L 52 15.82 -149.50 REMARK 500 ALA L 84 178.97 177.49 REMARK 500 SER L 90 -156.44 -143.52 REMARK 500 GLU L 198 -103.82 53.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH L 525 DISTANCE = 6.23 ANGSTROMS 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 NA L 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS H 1 O REMARK 620 2 THR L 5 OG1 19.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA L 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN L 37 OE1 REMARK 620 2 HOH L 507 O 84.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA L 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 81 OE2 REMARK 620 2 HOH L 511 O 113.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR G 191 OH REMARK 620 2 HOH G 305 O 108.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA L 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA G 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA F 201 DBREF 6VJN H -18 221 PDB 6VJN 6VJN -18 221 DBREF 6VJN L -18 212 PDB 6VJN 6VJN -18 212 DBREF 6VJN G 180 194 PDB 6VJN 6VJN 180 194 DBREF 6VJN F 180 194 PDB 6VJN 6VJN 180 194 SEQRES 1 H 241 MET GLY TRP SER CYS ILE ILE LEU PHE LEU VAL ALA THR SEQRES 2 H 241 ALA THR GLY VAL HIS SER HIS LEU GLN LEU GLN GLU SER SEQRES 3 H 241 GLY PRO GLY LEU VAL LYS PRO SER GLU THR LEU SER LEU SEQRES 4 H 241 THR CYS ALA VAL SER GLY GLY SER SER SER ASP TYR TRP SEQRES 5 H 241 TRP SER TRP ILE ARG GLN PRO PRO GLY LYS GLY LEU GLU SEQRES 6 H 241 TRP ILE GLY ARG ILE ASP SER ILE GLY ASN THR TYR TYR SEQRES 7 H 241 ASN PRO SER LEU ARG SER ARG VAL THR LEU SER VAL ASP SEQRES 8 H 241 THR SER LYS ASN GLN PHE SER LEU GLU LEU THR SER VAL SEQRES 9 H 241 THR ALA ALA ASP THR ALA VAL TYR TYR CYS ALA ARG PRO SEQRES 10 H 241 TYR CYS ALA ILE GLY ARG CYS TYR GLU SER TRP GLY GLN SEQRES 11 H 241 GLY VAL LEU VAL THR VAL SER SER ALA SER THR LYS GLY SEQRES 12 H 241 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SEQRES 13 H 241 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP SEQRES 14 H 241 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY SEQRES 15 H 241 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 16 H 241 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR SEQRES 17 H 241 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS SEQRES 18 H 241 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS SEQRES 19 H 241 ARG VAL GLU PRO LYS SER CYS SEQRES 1 L 236 MET GLY TRP SER CYS ILE ILE LEU PHE LEU VAL ALA THR SEQRES 2 L 236 ALA THR GLY SER VAL THR GLU VAL VAL PHE THR GLN PRO SEQRES 3 L 236 HIS SER VAL SER GLY SER PRO GLY GLN THR VAL THR ILE SEQRES 4 L 236 SER CYS THR ARG THR SER GLY SER ILE ASP SER GLU TYR SEQRES 5 L 236 VAL GLN TRP TYR GLN GLN ARG PRO GLY SER ALA PRO THR SEQRES 6 L 236 ILE VAL ILE TYR ARG ASP ASN GLN ARG PRO SER GLY VAL SEQRES 7 L 236 PRO ASP ARG PHE SER GLY SER ILE ASP SER SER SER ASN SEQRES 8 L 236 SER ALA SER LEU ALA ILE SER GLY LEU LYS SER GLU ASP SEQRES 9 L 236 GLU ALA ASP TYR TYR CYS GLN SER SER ASP ASP SER TYR SEQRES 10 L 236 ASN TRP VAL PHE GLY GLY GLY THR ARG LEU THR VAL LEU SEQRES 11 L 236 GLY GLN PRO LYS ALA ALA PRO SER VAL THR LEU PHE PRO SEQRES 12 L 236 PRO SER SER GLU GLU LEU GLN ALA ASN LYS ALA THR LEU SEQRES 13 L 236 VAL CYS LEU ILE SER ASP PHE TYR PRO GLY ALA VAL THR SEQRES 14 L 236 VAL ALA TRP LYS ALA ASP SER SER PRO VAL LYS ALA GLY SEQRES 15 L 236 VAL GLU THR THR THR PRO SER LYS GLN SER ASN ASN LYS SEQRES 16 L 236 TYR ALA ALA SER SER TYR LEU SER LEU THR PRO GLU GLN SEQRES 17 L 236 TRP LYS SER HIS ARG SER TYR SER CYS GLN VAL THR HIS SEQRES 18 L 236 GLU GLY SER THR VAL GLU LYS THR VAL ALA PRO THR GLU SEQRES 19 L 236 CYS SER SEQRES 1 G 19 ASP ILE VAL PRO LEU GLU GLU GLU ARG LYS GLY ASN SER SEQRES 2 G 19 SER LYS TYR ARG LEU ILE SEQRES 1 F 19 ASP ILE VAL PRO LEU GLU GLU GLU ARG LYS GLY ASN SER SEQRES 2 F 19 SER LYS TYR ARG LEU ILE HET NA H 301 1 HET NA L 301 1 HET NA L 302 1 HET NA L 303 1 HET NA G 201 1 HET NA F 201 1 HETNAM NA SODIUM ION FORMUL 5 NA 6(NA 1+) FORMUL 11 HOH *294(H2 O) HELIX 1 AA1 LEU H 63 SER H 65 5 3 HELIX 2 AA2 THR H 83 THR H 87 5 5 HELIX 3 AA3 SER H 159 ALA H 161 5 3 HELIX 4 AA4 SER H 192 LEU H 194 5 3 HELIX 5 AA5 LYS H 206 ASN H 209 5 4 HELIX 6 AA6 SER L 27B GLU L 31 5 5 HELIX 7 AA7 LYS L 79 GLU L 83 5 5 HELIX 8 AA8 SER L 121 ALA L 127 1 7 HELIX 9 AA9 THR L 181 HIS L 188 1 8 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O THR H 21 N SER H 7 SHEET 3 AA1 4 GLN H 77 LEU H 82 -1 O LEU H 82 N LEU H 18 SHEET 4 AA1 4 VAL H 67 ASP H 72 -1 N SER H 70 O SER H 79 SHEET 1 AA2 6 LEU H 11 VAL H 12 0 SHEET 2 AA2 6 VAL H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA2 6 ALA H 88 ALA H 98 -1 N ALA H 88 O VAL H 112 SHEET 4 AA2 6 TRP H 33 GLN H 39 -1 N ILE H 37 O TYR H 91 SHEET 5 AA2 6 GLU H 46 ASP H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O TYR H 58 N ARG H 50 SHEET 1 AA3 4 LEU H 11 VAL H 12 0 SHEET 2 AA3 4 VAL H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA3 4 ALA H 88 ALA H 98 -1 N ALA H 88 O VAL H 112 SHEET 4 AA3 4 ARG H 101 TRP H 106 -1 O TYR H 103 N TYR H 96 SHEET 1 AA4 4 SER H 123 LEU H 127 0 SHEET 2 AA4 4 THR H 138 TYR H 148 -1 O LYS H 146 N SER H 123 SHEET 3 AA4 4 TYR H 179 PRO H 190 -1 O VAL H 187 N LEU H 141 SHEET 4 AA4 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 AA5 4 SER H 123 LEU H 127 0 SHEET 2 AA5 4 THR H 138 TYR H 148 -1 O LYS H 146 N SER H 123 SHEET 3 AA5 4 TYR H 179 PRO H 190 -1 O VAL H 187 N LEU H 141 SHEET 4 AA5 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 AA6 3 THR H 154 TRP H 157 0 SHEET 2 AA6 3 TYR H 199 HIS H 205 -1 O ASN H 202 N SER H 156 SHEET 3 AA6 3 THR H 210 VAL H 216 -1 O VAL H 216 N TYR H 199 SHEET 1 AA7 4 PHE L 4 THR L 5 0 SHEET 2 AA7 4 VAL L 19 ARG L 25 -1 O THR L 24 N THR L 5 SHEET 3 AA7 4 SER L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 AA7 4 PHE L 62 ASP L 66A-1 N SER L 63 O ALA L 74 SHEET 1 AA8 5 SER L 9 GLY L 13 0 SHEET 2 AA8 5 THR L 102 VAL L 106 1 O ARG L 103 N VAL L 11 SHEET 3 AA8 5 ALA L 84 SER L 91 -1 N ALA L 84 O LEU L 104 SHEET 4 AA8 5 GLN L 34 GLN L 38 -1 N GLN L 34 O GLN L 89 SHEET 5 AA8 5 THR L 45 ILE L 48 -1 O VAL L 47 N TRP L 35 SHEET 1 AA9 4 SER L 9 GLY L 13 0 SHEET 2 AA9 4 THR L 102 VAL L 106 1 O ARG L 103 N VAL L 11 SHEET 3 AA9 4 ALA L 84 SER L 91 -1 N ALA L 84 O LEU L 104 SHEET 4 AA9 4 TRP L 96 PHE L 98 -1 O VAL L 97 N SER L 90 SHEET 1 AB1 4 SER L 114 PHE L 118 0 SHEET 2 AB1 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 AB1 4 TYR L 172 LEU L 180 -1 O SER L 176 N CYS L 134 SHEET 4 AB1 4 VAL L 159 THR L 161 -1 N GLU L 160 O TYR L 177 SHEET 1 AB2 4 SER L 114 PHE L 118 0 SHEET 2 AB2 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 AB2 4 TYR L 172 LEU L 180 -1 O SER L 176 N CYS L 134 SHEET 4 AB2 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 173 SHEET 1 AB3 4 PRO L 154 VAL L 155 0 SHEET 2 AB3 4 THR L 145 LYS L 149 -1 N TRP L 148 O VAL L 155 SHEET 3 AB3 4 TYR L 191 HIS L 197 -1 O GLN L 194 N ALA L 147 SHEET 4 AB3 4 SER L 200 VAL L 206 -1 O VAL L 202 N VAL L 195 SHEET 1 AB4 4 GLU F 186A GLU F 186A 0 SHEET 2 AB4 4 ILE G 181 PRO G 183 -1 N ILE G 181 O GLU F 186A SHEET 3 AB4 4 SER G 189 ILE G 194 -1 O ARG G 192 N VAL G 182 SHEET 4 AB4 4 TYR F 191 LEU F 193 1 O ARG F 192 N SER G 189 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.12 SSBOND 2 CYS H 97 CYS H 102 1555 1555 2.07 SSBOND 3 CYS H 143 CYS H 201 1555 1555 2.03 SSBOND 4 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 5 CYS L 134 CYS L 193 1555 1555 2.08 LINK O HIS H 1 NA NA L 303 1555 4545 2.86 LINK OG1 THR L 5 NA NA L 303 1555 1555 2.85 LINK OE1 GLN L 37 NA NA L 301 1555 1555 2.79 LINK OE2 GLU L 81 NA NA L 302 1555 1555 2.81 LINK NA NA L 301 O HOH L 507 1555 1555 2.52 LINK NA NA L 302 O HOH L 511 1555 1555 3.01 LINK OH TYR G 191 NA NA F 201 1555 1555 2.55 LINK NA NA G 201 O HOH G 303 1555 1555 3.16 LINK O HOH G 305 NA NA F 201 1555 1555 2.69 CISPEP 1 PHE H 149 PRO H 150 0 -8.95 CISPEP 2 GLU H 151 PRO H 152 0 1.35 CISPEP 3 TYR L 140 PRO L 141 0 -0.48 SITE 1 AC1 1 ALA H 84 SITE 1 AC2 3 GLN L 37 ARG L 39 HOH L 507 SITE 1 AC3 4 LYS L 79 SER L 80 GLU L 81 HOH L 511 SITE 1 AC4 4 HIS H 1 GLN H 3 GLY H 26 THR L 5 SITE 1 AC5 1 GLU G 185 SITE 1 AC6 4 SER F 189 LYS F 190 TYR G 191 HOH G 305 CRYST1 64.780 74.780 101.450 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 0.015437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009857 0.00000