HEADER IMMUNE SYSTEM 07-NOV-11 3UJJ TITLE CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 4025 IN COMPLEX WITH CON A TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 4025; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: FAB REGION OF THE HEAVY CHAIN OF ANTI-HIV-1 V3 MONOCLONAL COMPND 6 ANTIBODY 4025; COMPND 7 CHAIN: H; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: GP120; COMPND 10 CHAIN: P; COMPND 11 FRAGMENT: UNP RESIDUES 30-52; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 10 ORGANISM_TAXID: 11676; SOURCE 11 OTHER_DETAILS: SYNTHESIZED BASED ON HIV-1 STRAIN OF CONSENSUS CLADE SOURCE 12 A KEYWDS IG DOMAINS, ANTIBODY FAB, ANTIGEN BINDING, THE THIRD VARIABLE REGION KEYWDS 2 OF HIV-1 GP120, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.P.KONG,J.SAMPSON REVDAT 5 30-OCT-24 3UJJ 1 REMARK REVDAT 4 13-SEP-23 3UJJ 1 REMARK REVDAT 3 08-NOV-17 3UJJ 1 REMARK REVDAT 2 11-JAN-12 3UJJ 1 SEQRES REVDAT 1 28-DEC-11 3UJJ 0 JRNL AUTH M.K.GORNY,J.SAMPSON,H.LI,X.JIANG,M.TOTROV,X.H.WANG, JRNL AUTH 2 C.WILLIAMS,T.O'NEAL,B.VOLSKY,L.LI,T.CARDOZO,P.NYAMBI, JRNL AUTH 3 S.ZOLLA-PAZNER,X.P.KONG JRNL TITL HUMAN ANTI-V3 HIV-1 MONOCLONAL ANTIBODIES ENCODED BY THE JRNL TITL 2 VH5-51/VL LAMBDA GENES DEFINE A CONSERVED ANTIGENIC JRNL TITL 3 STRUCTURE. JRNL REF PLOS ONE V. 6 27780 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 22164215 JRNL DOI 10.1371/JOURNAL.PONE.0027780 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 52488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2665 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 39.3087 - 5.3254 1.00 2812 139 0.2004 0.2163 REMARK 3 2 5.3254 - 4.2285 1.00 2723 143 0.1463 0.1651 REMARK 3 3 4.2285 - 3.6944 1.00 2676 148 0.1411 0.1969 REMARK 3 4 3.6944 - 3.3569 1.00 2697 131 0.1564 0.1798 REMARK 3 5 3.3569 - 3.1164 1.00 2675 148 0.1603 0.2020 REMARK 3 6 3.1164 - 2.9327 1.00 2671 131 0.1692 0.1958 REMARK 3 7 2.9327 - 2.7859 1.00 2671 130 0.1734 0.2398 REMARK 3 8 2.7859 - 2.6646 1.00 2647 147 0.1766 0.2164 REMARK 3 9 2.6646 - 2.5621 1.00 2647 156 0.1813 0.2157 REMARK 3 10 2.5621 - 2.4737 1.00 2659 126 0.1750 0.2222 REMARK 3 11 2.4737 - 2.3963 1.00 2661 133 0.1872 0.2433 REMARK 3 12 2.3963 - 2.3278 1.00 2643 146 0.1934 0.2248 REMARK 3 13 2.3278 - 2.2666 1.00 2656 129 0.2046 0.2228 REMARK 3 14 2.2666 - 2.2113 1.00 2614 168 0.2059 0.2655 REMARK 3 15 2.2113 - 2.1610 0.99 2593 150 0.2112 0.2586 REMARK 3 16 2.1610 - 2.1150 0.99 2620 149 0.2157 0.2550 REMARK 3 17 2.1150 - 2.0727 0.96 2539 143 0.2326 0.2850 REMARK 3 18 2.0727 - 2.0336 0.90 2371 122 0.2495 0.2868 REMARK 3 19 2.0336 - 1.9973 0.85 2248 126 0.2817 0.3142 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 69.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.950 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) : -0.24040 REMARK 3 B22 (A**2) : -0.24040 REMARK 3 B33 (A**2) : 0.48430 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 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 : 0.007 3689 REMARK 3 ANGLE : 1.149 4979 REMARK 3 CHIRALITY : 0.078 536 REMARK 3 PLANARITY : 0.006 619 REMARK 3 DIHEDRAL : 12.622 1293 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3UJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97883 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: PDB ID 2B0S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 80 MM SODIUM REMARK 280 ACETATE, 30% GLYCEROL, PH 3.8, EVAPORATION, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.47033 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.94067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.94067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.47033 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 300 REMARK: THE FAB IS THE BIOLOGICAL ASSEMBLY AND THERE IS ONLY ONE REMARK 300 FAB IN THE ASYMMETRIC SUBUNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, P 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 ASN P 301 REMARK 465 ASN P 302 REMARK 465 ASP P 322 REMARK 465 ILE P 323 REMARK 465 ILE P 324 REMARK 465 GLY P 325 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 243 O HOH H 396 2.08 REMARK 500 O HOH L 390 O HOH H 378 2.08 REMARK 500 O HOH L 235 O HOH H 285 2.09 REMARK 500 O HOH H 241 O HOH H 333 2.11 REMARK 500 OH TYR L 89 O HOH L 267 2.14 REMARK 500 O HOH H 241 O HOH H 299 2.16 REMARK 500 O HOH L 305 O HOH L 338 2.16 REMARK 500 O HOH H 335 O HOH H 384 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 L 268 O HOH H 443 3564 2.09 REMARK 500 O HOH H 248 O HOH H 248 6555 2.10 REMARK 500 O THR L 209 O HOH P 251 5564 2.14 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 ASP L 51 -47.95 75.87 REMARK 500 SER L 52 -0.09 -142.68 REMARK 500 ASN L 170 -1.17 75.39 REMARK 500 GLU L 198 -109.37 57.22 REMARK 500 ASP H 144 60.41 62.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL L 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT L 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT L 227 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT L 228 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 227 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 228 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 229 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 231 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT H 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT H 234 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT H 235 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT P 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UJI RELATED DB: PDB DBREF 3UJJ P 301 325 UNP Q9YXJ8 Q9YXJ8_9HIV1 30 52 DBREF 3UJJ L 1 211 PDB 3UJJ 3UJJ 1 211 DBREF 3UJJ H 1 219 PDB 3UJJ 3UJJ 1 219 SEQRES 1 L 213 SER TYR GLU LEU THR GLN PRO PRO SER VAL SER VAL SER SEQRES 2 L 213 PRO GLY GLN THR ALA ARG ILE THR CYS SER GLY ASP ALA SEQRES 3 L 213 LEU PRO GLU LYS TYR ALA TYR TRP TYR GLN GLN LYS SER SEQRES 4 L 213 GLY GLN ALA PRO VAL LEU ILE ILE TYR GLU ASP SER LYS SEQRES 5 L 213 ARG PRO SER GLY ILE PRO GLU ARG PHE SER GLY SER ARG SEQRES 6 L 213 SER GLY THR MET ALA THR LEU THR ILE SER GLY ALA GLN SEQRES 7 L 213 VAL ASP ASP GLU ALA ASP TYR TYR CYS TYR SER THR ASN SEQRES 8 L 213 SER GLY GLY THR PHE PHE VAL PHE GLY THR GLY THR LYS SEQRES 9 L 213 VAL THR VAL LEU GLY GLN PRO LYS ALA ASN PRO THR VAL SEQRES 10 L 213 THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN SEQRES 11 L 213 LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO SEQRES 12 L 213 GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO SEQRES 13 L 213 VAL LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SEQRES 14 L 213 SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU SEQRES 15 L 213 THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS SEQRES 16 L 213 GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL SEQRES 17 L 213 ALA PRO THR GLU CYS SEQRES 1 H 230 GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 230 PRO GLY GLU SER LEU LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 230 TYR SER PHE SER SER TYR TRP ILE ALA TRP VAL ARG GLN SEQRES 4 H 230 MET PRO GLY LYS GLY LEU GLU TRP MET GLY PHE ILE TYR SEQRES 5 H 230 PRO ALA ASP SER ASP THR ARG TYR SER PRO SER PHE GLN SEQRES 6 H 230 GLY GLN GLY THR ILE SER ALA ASP LYS SER ILE SER THR SEQRES 7 H 230 ALA TYR LEU GLN TRP SER SER LEU LYS ALA SER ASP THR SEQRES 8 H 230 ALA MET TYR TYR CYS ALA ILE LEU GLY PHE TRP GLY ALA SEQRES 9 H 230 ASN ARG GLY GLY GLY GLY MET ASP VAL TRP GLY GLN GLY SEQRES 10 H 230 THR THR VAL ILE VAL SER SER ALA SER THR LYS GLY PRO SEQRES 11 H 230 SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER SEQRES 12 H 230 GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR SEQRES 13 H 230 PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA SEQRES 14 H 230 LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SEQRES 15 H 230 SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL SEQRES 16 H 230 PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN SEQRES 17 H 230 VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS SEQRES 18 H 230 VAL GLU PRO LYS SER CYS ASP LYS THR SEQRES 1 P 23 ASN ASN THR ARG LYS SER ILE ARG ILE GLY PRO GLY GLN SEQRES 2 P 23 ALA PHE TYR ALA THR GLY ASP ILE ILE GLY HET GOL L 212 6 HET GOL L 213 6 HET GOL L 214 6 HET GOL L 215 6 HET GOL L 216 6 HET GOL L 217 6 HET GOL L 218 6 HET GOL L 219 6 HET SO4 L 220 5 HET SO4 L 221 5 HET SO4 L 222 5 HET SO4 L 223 5 HET SO4 L 224 5 HET SO4 L 225 5 HET ACT L 226 4 HET ACT L 227 4 HET ACT L 228 4 HET GOL H 220 6 HET GOL H 221 6 HET GOL H 222 6 HET GOL H 223 6 HET GOL H 224 6 HET GOL H 225 6 HET GOL H 226 6 HET GOL H 227 6 HET GOL H 228 6 HET GOL H 229 6 HET GOL H 230 6 HET SO4 H 231 5 HET SO4 H 232 5 HET ACT H 233 4 HET ACT H 234 4 HET ACT H 235 4 HET ACT P 2 4 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 19(C3 H8 O3) FORMUL 12 SO4 8(O4 S 2-) FORMUL 18 ACT 7(C2 H3 O2 1-) FORMUL 38 HOH *489(H2 O) HELIX 1 1 GLN L 79 GLU L 83 5 5 HELIX 2 2 SER L 121 ALA L 127 1 7 HELIX 3 3 THR L 181 HIS L 188 1 8 HELIX 4 4 SER H 28 TYR H 32 5 5 HELIX 5 5 LYS H 73 ILE H 75 5 3 HELIX 6 6 LYS H 83 THR H 87 5 5 HELIX 7 7 TRP H 98 ARG H 100B 5 5 HELIX 8 8 SER H 187 LEU H 189 5 3 HELIX 9 9 LYS H 201 ASN H 204 5 4 SHEET 1 A 5 SER L 9 VAL L 13 0 SHEET 2 A 5 THR L 102 VAL L 106 1 O THR L 105 N VAL L 11 SHEET 3 A 5 ALA L 84 THR L 91 -1 N ALA L 84 O VAL L 104 SHEET 4 A 5 TYR L 34 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 A 5 VAL L 45 ILE L 48 -1 O ILE L 48 N TRP L 35 SHEET 1 B 4 SER L 9 VAL L 13 0 SHEET 2 B 4 THR L 102 VAL L 106 1 O THR L 105 N VAL L 11 SHEET 3 B 4 ALA L 84 THR L 91 -1 N ALA L 84 O VAL L 104 SHEET 4 B 4 PHE L 96 PHE L 98 -1 O VAL L 97 N SER L 90 SHEET 1 C 3 ALA L 19 SER L 24 0 SHEET 2 C 3 MET L 70 ILE L 75 -1 O ILE L 75 N ALA L 19 SHEET 3 C 3 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 D 4 THR L 114 PHE L 118 0 SHEET 2 D 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 D 4 TYR L 172 LEU L 180 -1 O ALA L 174 N ILE L 136 SHEET 4 D 4 VAL L 159 THR L 161 -1 N GLU L 160 O TYR L 177 SHEET 1 E 4 THR L 114 PHE L 118 0 SHEET 2 E 4 ALA L 130 PHE L 139 -1 O LEU L 135 N THR L 116 SHEET 3 E 4 TYR L 172 LEU L 180 -1 O ALA L 174 N ILE L 136 SHEET 4 E 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 173 SHEET 1 F 4 SER L 153 VAL L 155 0 SHEET 2 F 4 THR L 145 ALA L 150 -1 N ALA L 150 O SER L 153 SHEET 3 F 4 TYR L 191 HIS L 197 -1 O GLN L 194 N ALA L 147 SHEET 4 F 4 SER L 200 VAL L 206 -1 O VAL L 202 N VAL L 195 SHEET 1 G 4 GLN H 3 GLN H 6 0 SHEET 2 G 4 LEU H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 G 4 THR H 77 TRP H 82 -1 O LEU H 80 N ILE H 20 SHEET 4 G 4 THR H 68 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 H 6 GLU H 10 LYS H 12 0 SHEET 2 H 6 THR H 107 VAL H 111 1 O ILE H 110 N LYS H 12 SHEET 3 H 6 ALA H 88 LEU H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 H 6 ILE H 34 GLN H 39 -1 N GLN H 39 O MET H 89 SHEET 5 H 6 GLU H 46 TYR H 52 -1 O GLY H 49 N TRP H 36 SHEET 6 H 6 ASP H 56 TYR H 59 -1 O ARG H 58 N PHE H 50 SHEET 1 I 4 GLU H 10 LYS H 12 0 SHEET 2 I 4 THR H 107 VAL H 111 1 O ILE H 110 N LYS H 12 SHEET 3 I 4 ALA H 88 LEU H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 I 4 MET H 100G TRP H 103 -1 O VAL H 102 N ILE H 94 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 J 4 TYR H 176 PRO H 185 -1 O VAL H 182 N LEU H 138 SHEET 4 J 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 K 4 SER H 120 LEU H 124 0 SHEET 2 K 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 K 4 TYR H 176 PRO H 185 -1 O VAL H 182 N LEU H 138 SHEET 4 K 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 L 3 THR H 151 TRP H 154 0 SHEET 2 L 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 L 3 THR H 205 LYS H 210 -1 O THR H 205 N HIS H 200 SHEET 1 M 2 ARG P 308 GLY P 312 0 SHEET 2 M 2 GLN P 315 ALA P 316 -1 O GLN P 315 N ILE P 309 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.08 SSBOND 2 CYS L 134 CYS L 193 1555 1555 2.02 SSBOND 3 CYS L 211 CYS H 216 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 92 1555 1555 2.07 SSBOND 5 CYS H 140 CYS H 196 1555 1555 2.04 CISPEP 1 TYR L 140 PRO L 141 0 -2.16 CISPEP 2 SER H 132 GLY H 133 0 -15.53 CISPEP 3 PHE H 146 PRO H 147 0 -5.43 CISPEP 4 GLU H 148 PRO H 149 0 2.04 SITE 1 AC1 5 TYR L 2 ASN L 92 SER L 93 GLY L 94 SITE 2 AC1 5 HOH L 427 SITE 1 AC2 7 GLN L 37 VAL L 45 PRO L 59 HOH L 271 SITE 2 AC2 7 HOH L 302 HOH L 364 HOH L 397 SITE 1 AC3 8 ALA H 100 TYR L 49 ARG L 54 PRO L 55 SITE 2 AC3 8 SER L 56 HOH L 252 HOH L 333 HOH L 350 SITE 1 AC4 4 THR L 205 ACT L 228 HOH L 386 THR P 303 SITE 1 AC5 8 TYR H 91 GLN L 38 LYS L 39 GLY L 41 SITE 2 AC5 8 GLN L 42 HOH L 308 HOH L 327 HOH L 349 SITE 1 AC6 4 HOH H 339 SER L 121 SER L 122 HOH L 372 SITE 1 AC7 8 SER L 52 LYS L 53 ARG L 54 SO4 L 224 SITE 2 AC7 8 SO4 L 225 HOH L 304 HOH L 435 HOH L 468 SITE 1 AC8 7 HOH H 307 HOH H 325 GLN L 42 ALA L 43 SITE 2 AC8 7 VAL L 45 HOH L 283 HOH L 417 SITE 1 AC9 5 HIS H 164 GLN L 167 SER L 168 HOH L 341 SITE 2 AC9 5 HOH L 464 SITE 1 BC1 5 PRO L 59 ARG L 61 GLN L 79 ASP L 81 SITE 2 BC1 5 HOH L 271 SITE 1 BC2 5 SER L 40 GLU L 83 LYS L 103 TYR L 172 SITE 2 BC2 5 HOH L 359 SITE 1 BC3 4 PRO L 154 VAL L 155 LYS L 156 ALA L 157 SITE 1 BC4 5 ARG L 54 SER L 63 GOL L 218 HOH L 249 SITE 2 BC4 5 HOH L 276 SITE 1 BC5 6 LYS L 53 LYS L 186 ARG L 189 GOL L 218 SITE 2 BC5 6 HOH L 435 HOH L 468 SITE 1 BC6 3 THR L 18 ARG L 20 HOH L 434 SITE 1 BC7 4 ASN L 112 THR L 114 VAL L 115 LYS L 204 SITE 1 BC8 7 GLU L 198 GLY L 199 GLU L 203 THR L 205 SITE 2 BC8 7 GOL L 215 HOH L 474 ACT P 2 SITE 1 BC9 9 ALA H 125 SER H 127 ALA H 137 LYS H 214 SITE 2 BC9 9 HOH H 372 HOH H 412 LEU L 117 PHE L 118 SITE 3 BC9 9 PRO L 119 SITE 1 CC1 7 SER H 55 ASP H 56 THR H 57 HOH H 247 SITE 2 CC1 7 THR L 5 GLN L 6 THR L 100 SITE 1 CC2 8 SER H 130 THR H 131 SER H 132 GLY H 133 SITE 2 CC2 8 SER H 186 SER H 187 ACT H 233 HOH H 426 SITE 1 CC3 8 GLY H 65 GLN H 66 GLY H 67 TRP H 82 SITE 2 CC3 8 SER H 82A SER H 82B HOH H 368 HOH H 443 SITE 1 CC4 6 MET H 40 LYS H 43 GLY H 44 GLU H 46 SITE 2 CC4 6 HOH H 239 HOH L 438 SITE 1 CC5 6 LYS H 117 SER H 120 ASP H 144 HOH H 405 SITE 2 CC5 6 LYS L 129 HOH L 313 SITE 1 CC6 5 TYR H 27 SER H 28 PHE H 29 SER H 30 SITE 2 CC6 5 HOH H 323 SITE 1 CC7 10 GLY H 118 SER H 120 VAL H 121 PHE H 122 SITE 2 CC7 10 THR H 205 VAL H 207 LYS H 209 HOH H 248 SITE 3 CC7 10 HOH H 329 GLU L 123 SITE 1 CC8 6 LYS H 83 ALA H 84 SER H 85 HOH H 343 SITE 2 CC8 6 HOH H 373 HOH H 479 SITE 1 CC9 6 PRO H 41 LEU H 170 TYR H 176 HOH H 319 SITE 2 CC9 6 HOH H 370 HOH H 480 SITE 1 DC1 7 ARG H 38 SER H 62 PHE H 63 GLN H 66 SITE 2 DC1 7 LYS H 83 HOH H 299 HOH H 333 SITE 1 DC2 9 GLN H 171 SER H 172 HOH H 237 HOH H 298 SITE 2 DC2 9 HOH H 300 HOH H 303 GLY L 158 GLU L 160 SITE 3 DC2 9 SER L 179 SITE 1 DC3 5 TYR H 27 SER H 28 TYR H 32 HOH H 377 SITE 2 DC3 5 ARG P 304 SITE 1 DC4 7 SER H 127 SER H 128 LYS H 129 SER H 186 SITE 2 DC4 7 LEU H 189 THR H 219 GOL H 222 SITE 1 DC5 2 SER H 30 LYS H 73 SITE 1 DC6 2 GLY H 26 HOH H 421 SITE 1 DC7 3 ACT L 228 THR P 303 HOH P 414 CRYST1 136.143 136.143 73.411 90.00 90.00 120.00 P 31 2 1 6 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 0.007345 0.004241 0.000000 0.00000 SCALE2 0.000000 0.008482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013622 0.00000