HEADER VIRAL PROTEIN/IMMUNE SYSTEM 23-JUL-13 4LST TITLE CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC01 TITLE 2 IN COMPLEX WITH HIV-1 CLADE C STRAIN ZM176.66 GP120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE C; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF ANTIBODY VRC01; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF ANTIBODY VRC01; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: ZM176.66; SOURCE 5 GENE: ENV; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PVRC8400; SOURCE 18 MOL_ID: 3; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 23 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 24 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 25 EXPRESSION_SYSTEM_PLASMID: PVRC8400 KEYWDS NEUTRALIZING ANTIBODY VRC01, HIV ENVELOPE GLYCOPROTEIN GP120, KEYWDS 2 ANTIBODY ANTIGEN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,S.MOQUIN,P.D.KWONG REVDAT 6 27-NOV-24 4LST 1 HETSYN REVDAT 5 29-JUL-20 4LST 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 07-MAY-14 4LST 1 REMARK REVDAT 3 25-SEP-13 4LST 1 JRNL REVDAT 2 04-SEP-13 4LST 1 JRNL REVDAT 1 21-AUG-13 4LST 0 JRNL AUTH T.ZHOU,J.ZHU,X.WU,S.MOQUIN,B.ZHANG,P.ACHARYA,I.S.GEORGIEV, JRNL AUTH 2 H.R.ALTAE-TRAN,G.Y.CHUANG,M.G.JOYCE,Y.DO KWON,N.S.LONGO, JRNL AUTH 3 M.K.LOUDER,T.LUONGO,K.MCKEE,C.A.SCHRAMM,J.SKINNER,Y.YANG, JRNL AUTH 4 Z.YANG,Z.ZHANG,A.ZHENG,M.BONSIGNORI,B.F.HAYNES,J.F.SCHEID, JRNL AUTH 5 M.C.NUSSENZWEIG,M.SIMEK,D.R.BURTON,W.C.KOFF,J.C.MULLIKIN, JRNL AUTH 6 M.CONNORS,L.SHAPIRO,G.J.NABEL,J.R.MASCOLA,P.D.KWONG JRNL TITL MULTIDONOR ANALYSIS REVEALS STRUCTURAL ELEMENTS, GENETIC JRNL TITL 2 DETERMINANTS, AND MATURATION PATHWAY FOR HIV-1 JRNL TITL 3 NEUTRALIZATION BY VRC01-CLASS ANTIBODIES. JRNL REF IMMUNITY V. 39 245 2013 JRNL REFN ISSN 1074-7613 JRNL PMID 23911655 JRNL DOI 10.1016/J.IMMUNI.2013.04.012 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_998 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 32670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 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 40.6860 - 5.8379 0.95 2854 174 0.1786 0.1924 REMARK 3 2 5.8379 - 4.6358 0.98 2802 163 0.1573 0.2064 REMARK 3 3 4.6358 - 4.0504 0.99 2800 144 0.1478 0.2180 REMARK 3 4 4.0504 - 3.6803 0.99 2799 146 0.1865 0.2767 REMARK 3 5 3.6803 - 3.4167 1.00 2780 126 0.2088 0.2843 REMARK 3 6 3.4167 - 3.2153 0.99 2768 153 0.2253 0.2624 REMARK 3 7 3.2153 - 3.0544 0.99 2805 139 0.2420 0.3247 REMARK 3 8 3.0544 - 2.9214 0.99 2750 139 0.2620 0.3320 REMARK 3 9 2.9214 - 2.8090 0.96 2678 138 0.2772 0.3723 REMARK 3 10 2.8090 - 2.7121 0.87 2385 134 0.2833 0.3454 REMARK 3 11 2.7121 - 2.6273 0.71 1982 101 0.2834 0.3153 REMARK 3 12 2.6273 - 2.5522 0.58 1618 92 0.2841 0.3377 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 : 0.72 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 77.91 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 104.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.82650 REMARK 3 B22 (A**2) : 10.68710 REMARK 3 B33 (A**2) : -18.51350 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 : 0.004 6258 REMARK 3 ANGLE : 0.896 8487 REMARK 3 CHIRALITY : 0.060 954 REMARK 3 PLANARITY : 0.004 1083 REMARK 3 DIHEDRAL : 13.063 2305 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN G AND (RESID 44:253 OR RESID 476:492) REMARK 3 ORIGIN FOR THE GROUP (A): 34.0078 6.2309 6.4288 REMARK 3 T TENSOR REMARK 3 T11: 0.6193 T22: 0.8397 REMARK 3 T33: 0.5398 T12: -0.0719 REMARK 3 T13: 0.0754 T23: -0.0718 REMARK 3 L TENSOR REMARK 3 L11: 3.7690 L22: 7.3658 REMARK 3 L33: 4.3597 L12: -1.8219 REMARK 3 L13: 0.8241 L23: -2.1147 REMARK 3 S TENSOR REMARK 3 S11: 0.1035 S12: 0.1893 S13: 0.2463 REMARK 3 S21: -0.0405 S22: -0.2120 S23: -0.5556 REMARK 3 S31: 0.4682 S32: 0.6164 S33: 0.1597 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN G AND RESID 254:475 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5029 3.8492 5.1994 REMARK 3 T TENSOR REMARK 3 T11: 0.7244 T22: 0.6584 REMARK 3 T33: 0.5123 T12: -0.1054 REMARK 3 T13: -0.0162 T23: -0.1024 REMARK 3 L TENSOR REMARK 3 L11: 3.5649 L22: 3.7512 REMARK 3 L33: 6.3759 L12: 0.7037 REMARK 3 L13: -0.4043 L23: -1.7396 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: 0.6827 S13: -0.1497 REMARK 3 S21: -0.4521 S22: 0.1142 S23: 0.4140 REMARK 3 S31: 0.6567 S32: -0.2070 S33: -0.0285 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 1:114 REMARK 3 ORIGIN FOR THE GROUP (A): 6.2509 19.5715 27.2200 REMARK 3 T TENSOR REMARK 3 T11: 0.5341 T22: 0.5177 REMARK 3 T33: 0.4099 T12: -0.0615 REMARK 3 T13: -0.0535 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 7.5069 L22: 6.2977 REMARK 3 L33: 7.5836 L12: -2.0111 REMARK 3 L13: -0.3100 L23: 0.9662 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: -0.3422 S13: 0.6416 REMARK 3 S21: 0.3291 S22: -0.0417 S23: -0.0069 REMARK 3 S31: -0.2435 S32: -0.2617 S33: 0.0848 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND RESID 115:216 REMARK 3 ORIGIN FOR THE GROUP (A): -21.5184 19.9426 59.5296 REMARK 3 T TENSOR REMARK 3 T11: 1.1533 T22: 0.7194 REMARK 3 T33: 0.6714 T12: 0.0886 REMARK 3 T13: 0.0288 T23: -0.0631 REMARK 3 L TENSOR REMARK 3 L11: 9.2359 L22: 7.7928 REMARK 3 L33: 4.8544 L12: 2.1824 REMARK 3 L13: 1.2129 L23: -3.0118 REMARK 3 S TENSOR REMARK 3 S11: 0.1821 S12: -0.3290 S13: -0.0616 REMARK 3 S21: 0.4155 S22: 0.0855 S23: 0.4346 REMARK 3 S31: -0.1669 S32: -0.1626 S33: -0.2514 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:108 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0252 9.0388 46.3702 REMARK 3 T TENSOR REMARK 3 T11: 0.8609 T22: 0.6977 REMARK 3 T33: 0.4605 T12: 0.0170 REMARK 3 T13: -0.0710 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 7.1950 L22: 4.4976 REMARK 3 L33: 8.0259 L12: -1.6998 REMARK 3 L13: -2.7274 L23: -0.5424 REMARK 3 S TENSOR REMARK 3 S11: -0.2817 S12: -0.8379 S13: -0.1002 REMARK 3 S21: 0.8112 S22: 0.1112 S23: -0.1293 REMARK 3 S31: 0.7049 S32: 0.0671 S33: 0.1468 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 109:216 REMARK 3 ORIGIN FOR THE GROUP (A): -15.3270 5.1999 61.2530 REMARK 3 T TENSOR REMARK 3 T11: 1.3145 T22: 0.5597 REMARK 3 T33: 0.9336 T12: -0.0262 REMARK 3 T13: -0.2281 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 6.6162 L22: 2.0707 REMARK 3 L33: 5.8422 L12: 0.2726 REMARK 3 L13: 2.0439 L23: 1.2448 REMARK 3 S TENSOR REMARK 3 S11: 0.3926 S12: 0.1490 S13: -0.9810 REMARK 3 S21: -0.0534 S22: 0.3678 S23: 0.3032 REMARK 3 S31: 0.9185 S32: -0.1082 S33: -0.7240 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 4LST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000081041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : APS 22-BM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 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 (%): 59.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 11.8% PEG 4000, 0.2M NA REMARK 280 -ACETATE , PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 34.05250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 100.17550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.99050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 100.17550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.05250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.99050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, L 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 G 317 REMARK 465 GLY G 318 REMARK 465 GLY G 319 REMARK 465 SER G 320 REMARK 465 GLY G 321 REMARK 465 SER G 322 REMARK 465 GLY G 323 REMARK 465 GLY G 324 REMARK 465 THR G 402 REMARK 465 ALA G 403 REMARK 465 ASN G 404 REMARK 465 SER G 405 REMARK 465 THR G 406 REMARK 465 GLY G 407 REMARK 465 SER G 408 REMARK 465 VAL G 409 REMARK 465 THR H 131 REMARK 465 SER H 132 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 CG ASN G 230 C1 NAG G 503 1.81 REMARK 500 OD1 ASN G 230 C1 NAG G 503 1.82 REMARK 500 ND2 ASN G 339 C2 NAG G 508 2.16 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 LYS G 46 65.41 -157.71 REMARK 500 ASP G 211 108.05 -166.94 REMARK 500 PRO G 220 -177.36 -68.55 REMARK 500 GLN G 258 -58.26 63.11 REMARK 500 ASN G 276 112.86 -160.52 REMARK 500 ASN G 396 -173.82 -62.37 REMARK 500 THR G 412 123.87 75.26 REMARK 500 ASN G 463 -8.92 66.66 REMARK 500 CYS H 22 109.38 -165.54 REMARK 500 ASP H 85 0.41 -69.21 REMARK 500 PHE H 146 136.71 -170.62 REMARK 500 SER H 156 19.69 59.26 REMARK 500 GLN H 171 -177.09 -68.31 REMARK 500 SER H 188 32.07 -87.23 REMARK 500 TYR L 91 -126.01 55.01 REMARK 500 ASN L 140 72.03 43.98 REMARK 500 PRO L 143 -169.85 -73.87 REMARK 500 HIS L 191 143.55 69.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NGB RELATED DB: PDB REMARK 900 RELATED ID: 3SE8 RELATED DB: PDB REMARK 900 RELATED ID: 3SE9 RELATED DB: PDB REMARK 900 RELATED ID: 4JPV RELATED DB: PDB REMARK 900 RELATED ID: 4JPW RELATED DB: PDB REMARK 900 RELATED ID: 4JB9 RELATED DB: PDB REMARK 900 RELATED ID: 4J6R RELATED DB: PDB DBREF 4LST G 44 492 UNP R4GRV3 R4GRV3_9HIV1 1 355 DBREF 4LST H 1 216 PDB 4LST 4LST 1 216 DBREF 4LST L 1 216 PDB 4LST 4LST 1 216 SEQRES 1 G 355 VAL TRP LYS GLU ALA LYS THR THR LEU PHE CYS ALA SER SEQRES 2 G 355 ASP ALA LYS ALA TYR GLU ARG GLU VAL HIS ASN VAL TRP SEQRES 3 G 355 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 G 355 GLU MET ALA LEU GLY ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 G 355 TRP LYS ASN ASP MET VAL ASP GLN MET HIS GLU ASP ILE SEQRES 6 G 355 ILE SER LEU TRP ASP GLN SER LEU LYS PRO CYS VAL LYS SEQRES 7 G 355 LEU THR GLY GLY SER THR VAL THR GLN ALA CYS PRO LYS SEQRES 8 G 355 VAL SER PHE ASP PRO ILE PRO ILE HIS TYR CYS ALA PRO SEQRES 9 G 355 ALA GLY TYR ALA ILE LEU LYS CYS ASN ASN GLU THR PHE SEQRES 10 G 355 GLU GLY THR GLY PRO CYS ASN ASN VAL SER THR VAL GLN SEQRES 11 G 355 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 G 355 LEU LEU ASN GLY SER LEU ALA LYS GLU GLU ILE VAL ILE SEQRES 13 G 355 ARG SER GLU ASN LEU THR ASP ASN ALA LYS THR ILE ILE SEQRES 14 G 355 VAL HIS LEU LYS GLU SER VAL GLU ILE VAL CYS THR ARG SEQRES 15 G 355 PRO GLY ASN GLY GLY SER GLY SER GLY GLY ASP THR ARG SEQRES 16 G 355 GLN ALA HIS CYS ASN ILE SER GLU GLU LYS TRP ASN LYS SEQRES 17 G 355 THR LEU GLN LYS VAL SER LYS ILE LEU GLN GLU HIS PHE SEQRES 18 G 355 PRO ASN LYS ALA ILE LYS PHE GLU PRO HIS SER GLY GLY SEQRES 19 G 355 ASP LEU GLU ILE THR THR HIS SER PHE ASN CYS ARG GLY SEQRES 20 G 355 GLU PHE PHE TYR CYS ASN THR THR LYS LEU PHE ASN GLY SEQRES 21 G 355 THR TYR ASN SER THR ALA ASN SER THR GLY SER VAL SER SEQRES 22 G 355 ASN THR THR ILE THR LEU PRO CYS ARG ILE LYS GLN ILE SEQRES 23 G 355 VAL ASN MET TRP GLN GLY VAL GLY ARG ALA MET TYR ALA SEQRES 24 G 355 PRO PRO ILE LYS GLY ASN ILE THR CYS LYS SER ILE ILE SEQRES 25 G 355 THR GLY LEU LEU LEU THR ARG ASP GLY GLY ASN ASP ASP SEQRES 26 G 355 ASN ASP THR GLU THR PHE ARG PRO GLY GLY GLY ASP MET SEQRES 27 G 355 ARG ASP ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL SEQRES 28 G 355 VAL GLU ILE LYS SEQRES 1 H 224 GLN VAL GLN LEU VAL GLN SER GLY GLY GLN MET LYS LYS SEQRES 2 H 224 PRO GLY GLU SER MET ARG ILE SER CYS ARG ALA SER GLY SEQRES 3 H 224 TYR GLU PHE ILE ASP CYS THR LEU ASN TRP ILE ARG LEU SEQRES 4 H 224 ALA PRO GLY LYS ARG PRO GLU TRP MET GLY TRP LEU LYS SEQRES 5 H 224 PRO ARG GLY GLY ALA VAL ASN TYR ALA ARG PRO LEU GLN SEQRES 6 H 224 GLY ARG VAL THR MET THR ARG ASP VAL TYR SER ASP THR SEQRES 7 H 224 ALA PHE LEU GLU LEU ARG SER LEU THR VAL ASP ASP THR SEQRES 8 H 224 ALA VAL TYR PHE CYS THR ARG GLY LYS ASN CYS ASP TYR SEQRES 9 H 224 ASN TRP ASP PHE GLU HIS TRP GLY ARG GLY THR PRO VAL SEQRES 10 H 224 ILE VAL SER SER PRO SER THR LYS GLY PRO SER VAL PHE SEQRES 11 H 224 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR SEQRES 12 H 224 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU SEQRES 13 H 224 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER SEQRES 14 H 224 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY SEQRES 15 H 224 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SEQRES 16 H 224 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS SEQRES 17 H 224 LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO SEQRES 18 H 224 LYS SER CYS SEQRES 1 L 210 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 210 SER PRO GLY GLU THR ALA ILE ILE SER CYS ARG THR SER SEQRES 3 L 210 GLN TYR GLY SER LEU ALA TRP TYR GLN GLN ARG PRO GLY SEQRES 4 L 210 GLN ALA PRO ARG LEU VAL ILE TYR SER GLY SER THR ARG SEQRES 5 L 210 ALA ALA GLY ILE PRO ASP ARG PHE SER GLY SER ARG TRP SEQRES 6 L 210 GLY PRO ASP TYR ASN LEU THR ILE SER ASN LEU GLU SER SEQRES 7 L 210 GLY ASP PHE GLY VAL TYR TYR CYS GLN GLN TYR GLU PHE SEQRES 8 L 210 PHE GLY GLN GLY THR LYS VAL GLN VAL ASP ILE LYS ARG SEQRES 9 L 210 THR VAL ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER SEQRES 10 L 210 ASP GLU GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS SEQRES 11 L 210 LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN SEQRES 12 L 210 TRP LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN SEQRES 13 L 210 GLU SER VAL THR GLU GLN ASP SER LYS ASP SER THR TYR SEQRES 14 L 210 SER LEU SER SER THR LEU THR LEU SER LYS ALA ASP TYR SEQRES 15 L 210 GLU LYS HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN SEQRES 16 L 210 GLY LEU ARG SER PRO VAL THR LYS SER PHE ASN ARG GLY SEQRES 17 L 210 GLU CYS MODRES 4LST ASN G 396 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 276 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 339 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 241 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 230 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 386 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 392 ASN GLYCOSYLATION SITE MODRES 4LST ASN G 262 ASN GLYCOSYLATION SITE HET NAG G 501 14 HET NAG G 502 14 HET NAG G 503 14 HET NAG G 504 14 HET NAG G 505 14 HET NAG G 506 14 HET NAG G 507 14 HET NAG G 508 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 4 NAG 8(C8 H15 N O6) FORMUL 12 HOH *71(H2 O) HELIX 1 1 GLU G 64 CYS G 74 1 11 HELIX 2 2 ASN G 98 LEU G 116 1 19 HELIX 3 3 GLU G 335 PHE G 353 1 19 HELIX 4 4 ASP G 368 THR G 373 1 6 HELIX 5 5 THR G 387 PHE G 391 5 5 HELIX 6 6 MET G 475 TYR G 484 1 10 HELIX 7 7 GLU H 28 CYS H 32 5 5 HELIX 8 8 ARG H 61 GLN H 64 5 4 HELIX 9 9 THR H 83 THR H 87 5 5 HELIX 10 10 SER H 156 ALA H 158 5 3 HELIX 11 11 LYS H 201 ASN H 204 5 4 HELIX 12 12 GLU L 79 PHE L 83 5 5 HELIX 13 13 SER L 123 LYS L 128 1 6 HELIX 14 14 LYS L 185 LYS L 190 1 6 SHEET 1 A 2 PHE G 53 ALA G 55 0 SHEET 2 A 2 HIS G 216 CYS G 218 -1 O HIS G 216 N ALA G 55 SHEET 1 B 4 MET G 84 LEU G 86 0 SHEET 2 B 4 VAL G 242 VAL G 245 -1 O THR G 244 N MET G 84 SHEET 3 B 4 TYR G 223 CYS G 228 -1 N ILE G 225 O VAL G 245 SHEET 4 B 4 TYR G 486 GLU G 490 -1 O LYS G 487 N LEU G 226 SHEET 1 C 2 GLU G 91 ASN G 94 0 SHEET 2 C 2 THR G 236 CYS G 239 -1 O GLY G 237 N PHE G 93 SHEET 1 D 4 SER G 199 VAL G 201 0 SHEET 2 D 4 VAL G 120 THR G 123 -1 N LYS G 121 O VAL G 201 SHEET 3 D 4 ARG G 432 MET G 434 -1 O MET G 434 N VAL G 120 SHEET 4 D 4 ILE G 423 ASN G 425 -1 N VAL G 424 O ALA G 433 SHEET 1 E 5 LEU G 259 LEU G 261 0 SHEET 2 E 5 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260 SHEET 3 E 5 ILE G 284 ARG G 298 -1 N VAL G 292 O ILE G 449 SHEET 4 E 5 THR G 465 PRO G 470 0 SHEET 5 E 5 ALA G 358 PHE G 361 1 N ALA G 358 O GLU G 466 SHEET 1 F 7 VAL G 271 ARG G 273 0 SHEET 2 F 7 ILE G 284 ARG G 298 -1 O ILE G 285 N ARG G 273 SHEET 3 F 7 ILE G 443 ARG G 456 -1 O ILE G 449 N VAL G 292 SHEET 4 F 7 GLN G 328 SER G 334 0 SHEET 5 F 7 THR G 413 LYS G 421 -1 O ILE G 414 N ILE G 333 SHEET 6 F 7 GLU G 381 CYS G 385 -1 N PHE G 382 O LYS G 421 SHEET 7 F 7 HIS G 374 CYS G 378 -1 N CYS G 378 O GLU G 381 SHEET 1 G 4 GLN H 3 GLN H 6 0 SHEET 2 G 4 MET H 18 SER H 25 -1 O ARG H 23 N VAL H 5 SHEET 3 G 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 G 4 VAL H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 H 6 GLN 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 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 H 6 LEU H 34 LEU H 39 -1 N ILE H 37 O PHE H 91 SHEET 5 H 6 GLU H 46 LYS H 52 -1 O MET H 48 N TRP H 36 SHEET 6 H 6 ALA H 56 TYR H 59 -1 O ALA H 56 N LYS H 52 SHEET 1 I 4 GLN 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 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 I 4 HIS H 102 TRP H 103 -1 O HIS H 102 N ARG H 94 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 J 4 TYR H 176 VAL H 184 -1 O TYR H 176 N TYR H 145 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 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 K 4 TYR H 176 VAL H 184 -1 O TYR H 176 N TYR H 145 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 LYS H 209 N CYS H 196 SHEET 1 M 4 LEU L 4 SER L 7 0 SHEET 2 M 4 ALA L 19 THR L 25 -1 O SER L 22 N SER L 7 SHEET 3 M 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 M 4 PHE L 62 TRP L 67 -1 N TRP L 67 O ASP L 70 SHEET 1 N 6 THR L 10 LEU L 13 0 SHEET 2 N 6 THR L 102 VAL L 106 1 O LYS L 103 N LEU L 11 SHEET 3 N 6 GLY L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 N 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 N 6 ARG L 45 TYR L 49 -1 O VAL L 47 N TRP L 35 SHEET 6 N 6 THR L 53 ARG L 54 -1 O THR L 53 N TYR L 49 SHEET 1 O 4 THR L 10 LEU L 13 0 SHEET 2 O 4 THR L 102 VAL L 106 1 O LYS L 103 N LEU L 11 SHEET 3 O 4 GLY L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 O 4 PHE L 97 PHE L 98 -1 O PHE L 97 N GLN L 90 SHEET 1 P 4 SER L 116 PHE L 120 0 SHEET 2 P 4 THR L 131 PHE L 141 -1 O LEU L 137 N PHE L 118 SHEET 3 P 4 TYR L 175 SER L 184 -1 O LEU L 183 N ALA L 132 SHEET 4 P 4 SER L 161 GLN L 162 -1 N GLN L 162 O THR L 180 SHEET 1 Q 3 LYS L 147 VAL L 152 0 SHEET 2 Q 3 VAL L 193 THR L 199 -1 O GLU L 197 N GLN L 149 SHEET 3 Q 3 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198 SSBOND 1 CYS G 54 CYS G 74 1555 1555 2.04 SSBOND 2 CYS G 119 CYS G 205 1555 1555 2.03 SSBOND 3 CYS G 218 CYS G 247 1555 1555 2.04 SSBOND 4 CYS G 228 CYS G 239 1555 1555 2.04 SSBOND 5 CYS G 296 CYS G 331 1555 1555 2.03 SSBOND 6 CYS G 378 CYS G 445 1555 1555 2.03 SSBOND 7 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 8 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 9 CYS H 32 CYS H 98 1555 1555 2.04 SSBOND 10 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 11 CYS H 216 CYS L 216 1555 1555 2.03 SSBOND 12 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 13 CYS L 136 CYS L 196 1555 1555 2.04 LINK ND2 ASN G 230 C1 NAG G 503 1555 1555 1.44 LINK ND2 ASN G 241 C1 NAG G 504 1555 1555 1.44 LINK ND2 ASN G 262 C1 NAG G 501 1555 1555 1.45 LINK ND2 ASN G 276 C1 NAG G 502 1555 1555 1.44 LINK ND2 ASN G 339 C1 NAG G 508 1555 1555 1.44 LINK ND2 ASN G 386 C1 NAG G 505 1555 1555 1.44 LINK ND2 ASN G 392 C1 NAG G 507 1555 1555 1.45 LINK ND2 ASN G 396 C1 NAG G 506 1555 1555 1.44 CISPEP 1 PHE H 146 PRO H 147 0 -9.26 CISPEP 2 GLU H 148 PRO H 149 0 5.30 CISPEP 3 SER L 7 PRO L 8 0 0.36 CISPEP 4 TYR L 142 PRO L 143 0 3.58 CRYST1 68.105 77.981 200.351 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 0.014683 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004991 0.00000