HEADER VIRAL PROTEIN/IMMUNE SYSTEM 20-OCT-17 6BCK TITLE CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING ANTIBODY N49P7 IN COMPLEX TITLE 2 WITH HIV-1 CLADE AE STRAIN 93TH057 GP120 CORE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLADE A/E 93TH057 HIV-1 GP120 CORE; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: N49P7 FAB HEAVY CHAIN OF N29P7 IGG; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: N49P7 FAB LIGHT CHAIN FROM N49P7 IGG; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: HIV-1 ENV; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HEK 293; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: HEK 293; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: HEK 293; SOURCE 22 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HIV-1, VRC01-CLASS ANTIBODY, CD4 BINDING SITE, CLADE A/E 93TH057 KEYWDS 2 GP120, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, N49P7, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR W.D.TOLBERT,N.GOHAIN,M.PAZGIER REVDAT 6 04-OCT-23 6BCK 1 HETSYN REVDAT 5 29-JUL-20 6BCK 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 11-DEC-19 6BCK 1 REMARK REVDAT 3 20-FEB-19 6BCK 1 REMARK REVDAT 2 27-JUN-18 6BCK 1 JRNL REVDAT 1 23-MAY-18 6BCK 0 JRNL AUTH M.M.SAJADI,A.DASHTI,Z.RIKHTEGARAN TEHRANI,W.D.TOLBERT, JRNL AUTH 2 M.S.SEAMAN,X.OUYANG,N.GOHAIN,M.PAZGIER,D.KIM,G.CAVET, JRNL AUTH 3 J.YARED,R.R.REDFIELD,G.K.LEWIS,A.L.DEVICO JRNL TITL IDENTIFICATION OF NEAR-PAN-NEUTRALIZING ANTIBODIES AGAINST JRNL TITL 2 HIV-1 BY DECONVOLUTION OF PLASMA HUMORAL RESPONSES. JRNL REF CELL V. 173 1783 2018 JRNL REFN ISSN 1097-4172 JRNL PMID 29731169 JRNL DOI 10.1016/J.CELL.2018.03.061 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 63.1 REMARK 3 NUMBER OF REFLECTIONS : 18015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 919 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 44.2670 - 5.1626 0.79 3243 172 0.2178 0.2656 REMARK 3 2 5.1626 - 4.0987 0.81 3167 176 0.1891 0.2234 REMARK 3 3 4.0987 - 3.5808 0.83 3181 177 0.2119 0.3052 REMARK 3 4 3.5808 - 3.2535 0.68 2599 145 0.2452 0.2978 REMARK 3 5 3.2535 - 3.0204 0.54 2059 111 0.2604 0.3536 REMARK 3 6 3.0204 - 2.8424 0.43 1627 82 0.3243 0.3967 REMARK 3 7 2.8424 - 2.7000 0.32 1220 56 0.3553 0.4211 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.410 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 : 0.014 6151 REMARK 3 ANGLE : 1.163 8395 REMARK 3 CHIRALITY : 0.076 964 REMARK 3 PLANARITY : 0.009 1069 REMARK 3 DIHEDRAL : 8.460 3622 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'G' AND RESID 44 THROUGH 491) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1269 5.9501 -56.5601 REMARK 3 T TENSOR REMARK 3 T11: -0.5867 T22: -0.2717 REMARK 3 T33: 0.2142 T12: 0.1309 REMARK 3 T13: -0.1417 T23: -0.0394 REMARK 3 L TENSOR REMARK 3 L11: 0.0304 L22: 0.0492 REMARK 3 L33: -0.0313 L12: -0.0057 REMARK 3 L13: 0.0096 L23: -0.0019 REMARK 3 S TENSOR REMARK 3 S11: -0.0680 S12: 0.1432 S13: -0.0340 REMARK 3 S21: 0.0522 S22: 0.0051 S23: -0.2627 REMARK 3 S31: 0.0037 S32: -0.1871 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'H' AND RESID 2 THROUGH 212) REMARK 3 ORIGIN FOR THE GROUP (A): -39.5219 -18.2398 -25.3278 REMARK 3 T TENSOR REMARK 3 T11: 0.0736 T22: 0.1329 REMARK 3 T33: -0.7795 T12: 0.0626 REMARK 3 T13: 0.4950 T23: -0.0817 REMARK 3 L TENSOR REMARK 3 L11: -0.0379 L22: -0.0323 REMARK 3 L33: 0.0009 L12: 0.0224 REMARK 3 L13: -0.0246 L23: -0.0335 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: 0.0629 S13: 0.0348 REMARK 3 S21: 0.1198 S22: -0.1183 S23: -0.0422 REMARK 3 S31: 0.0918 S32: -0.0392 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'L' AND RESID 3 THROUGH 208) REMARK 3 ORIGIN FOR THE GROUP (A): -29.9830 -14.2121 -11.9590 REMARK 3 T TENSOR REMARK 3 T11: 0.6185 T22: 0.3297 REMARK 3 T33: 0.1570 T12: 0.1393 REMARK 3 T13: 0.0978 T23: -0.0318 REMARK 3 L TENSOR REMARK 3 L11: -0.0171 L22: 0.0034 REMARK 3 L33: 0.0279 L12: 0.0242 REMARK 3 L13: -0.0089 L23: -0.0121 REMARK 3 S TENSOR REMARK 3 S11: -0.1141 S12: -0.0204 S13: -0.2886 REMARK 3 S21: 0.0628 S22: 0.0500 S23: 0.0810 REMARK 3 S31: -0.0470 S32: -0.0216 S33: -0.0000 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 6BCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : RH COATED FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23639 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 44.261 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.74900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.070 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: 3TGT, 3TNN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 5000 MME 12% ISOPROPANOL 0.1 M REMARK 280 MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.71800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 127.64250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.93350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 127.64250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.71800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.93350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY G 403 REMARK 465 ASN G 404 REMARK 465 GLU G 405 REMARK 465 THR G 406 REMARK 465 MET G 407 REMARK 465 LYS G 408 REMARK 465 GLY G 409 REMARK 465 GLU G 492 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 PRO H 213 REMARK 465 LYS H 214 REMARK 465 GLN L 1 REMARK 465 SER L 2 REMARK 465 THR L 209 REMARK 465 GLU L 210 REMARK 465 CYS L 211 REMARK 465 SER L 212 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 SG CYS H 22 SG CYS H 92 1.65 REMARK 500 ND2 ASN G 276 C1 NAG G 504 1.96 REMARK 500 N THR L 70 O HOH L 301 2.11 REMARK 500 O PRO G 118 NE2 GLN G 203 2.16 REMARK 500 ND2 ASN G 289 C2 NAG G 505 2.17 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 G 331 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 CYS G 395 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 CYS H 140 CA - CB - SG ANGL. DEV. = -13.3 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 LEU G 86 78.29 -114.50 REMARK 500 ASP G 211 109.27 -160.98 REMARK 500 PRO G 220 -158.58 -77.89 REMARK 500 ASP G 230 109.20 -59.13 REMARK 500 GLN G 258 -58.36 62.03 REMARK 500 GLU G 268 -77.61 -104.96 REMARK 500 ASN G 355 -10.24 57.15 REMARK 500 PHE G 391 66.24 -105.58 REMARK 500 ASN G 411 27.03 -164.89 REMARK 500 CYS G 445 91.92 -161.47 REMARK 500 LYS G 487 108.95 -164.03 REMARK 500 ASP H 16 179.47 59.76 REMARK 500 TYR H 32 122.83 67.06 REMARK 500 LYS H 62 -26.62 -34.71 REMARK 500 LYS H 83 -157.35 -118.27 REMARK 500 GLU H 100E 82.28 79.20 REMARK 500 SER H 113 31.88 -76.88 REMARK 500 ALA H 114 -155.42 -100.47 REMARK 500 SER H 115 -89.02 -151.77 REMARK 500 THR H 116 -80.73 -149.93 REMARK 500 LYS H 117 -178.77 60.07 REMARK 500 SER H 127 -107.93 -138.10 REMARK 500 ALA H 136 117.00 -160.28 REMARK 500 ASP H 144 81.15 58.37 REMARK 500 PHE H 146 133.63 -172.01 REMARK 500 PRO H 147 -163.83 -103.04 REMARK 500 ASN H 204 76.86 52.01 REMARK 500 THR L 5 -84.33 -60.09 REMARK 500 GLN L 6 118.68 68.13 REMARK 500 PRO L 15 71.55 -43.08 REMARK 500 GLN L 17 -138.40 -88.24 REMARK 500 HIS L 27 40.06 -73.52 REMARK 500 PRO L 40 104.09 -56.68 REMARK 500 PHE L 51 -76.97 68.91 REMARK 500 PRO L 55 -158.70 -71.52 REMARK 500 SER L 65 -169.53 -166.07 REMARK 500 SER L 67 144.26 -179.33 REMARK 500 ASP L 83 94.72 -68.44 REMARK 500 TYR L 91 -118.49 56.04 REMARK 500 ASP L 138 71.75 44.78 REMARK 500 ASP L 151 -84.06 47.36 REMARK 500 THR L 161 -152.17 -90.12 REMARK 500 ASN L 169 37.42 -144.44 REMARK 500 LYS L 171 -169.79 -108.56 REMARK 500 HIS L 188 -153.74 -143.13 REMARK 500 GLU L 198 71.30 16.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU G 275 ASN G 276 149.57 REMARK 500 GLY H 139 CYS H 140 -149.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG G 504 DBREF1 6BCK G 44 492 UNP A0A0M3KKW9_9HIV1 DBREF2 6BCK G A0A0M3KKW9 1 353 DBREF 6BCK H 2 214 PDB 6BCK 6BCK 2 214 DBREF 6BCK L 1 212 PDB 6BCK 6BCK 1 212 SEQADV 6BCK SER G 375 UNP A0A0M3KKW HIS 242 ENGINEERED MUTATION SEQRES 1 G 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 G 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 G 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 G 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 G 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 G 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 G 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 G 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 G 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 G 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 G 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 G 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 G 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 G 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 G 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 G 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 G 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 G 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 G 353 ASP LEU GLU ILE THR MET HIS SER PHE ASN CYS ARG GLY SEQRES 20 G 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 G 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 G 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 G 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 G 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 G 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 G 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 G 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 G 353 ILE GLU SEQRES 1 H 228 ALA ASP LEU VAL GLN SER GLY ALA VAL VAL LYS LYS PRO SEQRES 2 H 228 GLY ASP SER VAL ARG ILE SER CYS GLU ALA GLN GLY TYR SEQRES 3 H 228 ARG PHE PRO ASP TYR ILE ILE HIS TRP ILE ARG ARG ALA SEQRES 4 H 228 PRO GLY GLN GLY PRO GLU TRP MET GLY TRP MET ASN PRO SEQRES 5 H 228 MET GLY GLY GLN VAL ASN ILE PRO TRP LYS PHE GLN GLY SEQRES 6 H 228 ARG VAL SER MET THR ARG ASP THR SER ILE GLU THR ALA SEQRES 7 H 228 PHE LEU ASP LEU ARG GLY LEU LYS SER ASP ASP THR ALA SEQRES 8 H 228 VAL TYR TYR CYS VAL ARG ASP ARG SER ASN GLY SER GLY SEQRES 9 H 228 LYS ARG PHE GLU SER SER ASN TRP PHE LEU ASP LEU TRP SEQRES 10 H 228 GLY ARG GLY THR ALA VAL THR ILE GLN SER ALA SER THR SEQRES 11 H 228 LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SEQRES 12 H 228 SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL SEQRES 13 H 228 LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SEQRES 14 H 228 SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA SEQRES 15 H 228 VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL SEQRES 16 H 228 VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR SEQRES 17 H 228 ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL SEQRES 18 H 228 ASP LYS ARG VAL GLU PRO LYS SEQRES 1 L 205 GLN SER ALA LEU THR GLN PRO ARG SER VAL SER ALA SER SEQRES 2 L 205 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR HIS SEQRES 3 L 205 ASN LEU VAL SER TRP CYS GLN HIS GLN PRO GLY ARG ALA SEQRES 4 L 205 PRO LYS LEU LEU ILE TYR ASP PHE ASN LYS ARG PRO SER SEQRES 5 L 205 GLY VAL PRO ASP ARG PHE SER GLY SER GLY SER GLY GLY SEQRES 6 L 205 THR ALA SER LEU THR ILE THR GLY LEU GLN ASP ASP ASP SEQRES 7 L 205 ASP ALA GLU TYR PHE CYS TRP ALA TYR GLU ALA PHE GLY SEQRES 8 L 205 GLY GLY THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA SEQRES 9 L 205 ALA PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU SEQRES 10 L 205 LEU GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER SEQRES 11 L 205 ASP PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA SEQRES 12 L 205 ASP SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR SEQRES 13 L 205 PRO SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER SEQRES 14 L 205 TYR LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SEQRES 15 L 205 SER TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL SEQRES 16 L 205 GLU LYS THR VAL ALA PRO THR GLU CYS SER 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 HET NAG G 509 14 HET NAG G 510 14 HET NAG G 511 14 HET MPD G 512 8 HET MPD H 301 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL 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 11(C8 H15 N O6) FORMUL 15 MPD 2(C6 H14 O2) FORMUL 17 HOH *27(H2 O) HELIX 1 AA1 GLU G 64 CYS G 74 1 11 HELIX 2 AA2 ASN G 98 LEU G 116 1 19 HELIX 3 AA3 GLY G 335 PHE G 353 1 19 HELIX 4 AA4 ASP G 368 MET G 373 1 6 HELIX 5 AA5 THR G 387 PHE G 391 5 5 HELIX 6 AA6 ILE G 475 TYR G 484 1 10 HELIX 7 AA7 PRO H 60 GLN H 64 5 5 HELIX 8 AA8 SER H 153 GLY H 157 5 5 HELIX 9 AA9 PRO H 185 LEU H 189 5 5 HELIX 10 AB1 SER L 121 ALA L 127 1 7 HELIX 11 AB2 THR L 181 LYS L 186 1 6 SHEET 1 AA1 5 LYS G 46 ASP G 47 0 SHEET 2 AA1 5 TYR G 486 GLN G 490 -1 O GLN G 490 N LYS G 46 SHEET 3 AA1 5 TYR G 223 CYS G 228 -1 N VAL G 224 O VAL G 489 SHEET 4 AA1 5 VAL G 242 VAL G 245 -1 O VAL G 245 N ILE G 225 SHEET 5 AA1 5 ILE G 84 HIS G 85 -1 N ILE G 84 O SER G 244 SHEET 1 AA2 3 VAL G 75 PRO G 76 0 SHEET 2 AA2 3 PHE G 53 SER G 56 1 N SER G 56 O VAL G 75 SHEET 3 AA2 3 HIS G 216 CYS G 218 -1 O HIS G 216 N ALA G 55 SHEET 1 AA3 2 GLU G 91 ASN G 92 0 SHEET 2 AA3 2 PRO G 238 CYS G 239 -1 O CYS G 239 N GLU G 91 SHEET 1 AA4 4 SER G 199 LYS G 202 0 SHEET 2 AA4 4 VAL G 120 THR G 123 -1 N LYS G 121 O ILE G 201 SHEET 3 AA4 4 GLN G 432 MET G 434 -1 O GLN G 432 N LEU G 122 SHEET 4 AA4 4 ILE G 423 ASN G 425 -1 N ILE G 424 O ALA G 433 SHEET 1 AA5 4 LEU G 259 LEU G 261 0 SHEET 2 AA5 4 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260 SHEET 3 AA5 4 ASN G 465 PRO G 470 -1 O ARG G 469 N THR G 455 SHEET 4 AA5 4 THR G 358 PHE G 361 1 N ILE G 360 O GLU G 466 SHEET 1 AA6 8 ILE G 271 ARG G 273 0 SHEET 2 AA6 8 ILE G 284 HIS G 287 -1 O ILE G 285 N ARG G 273 SHEET 3 AA6 8 ILE G 443 ARG G 456 -1 O ILE G 452 N VAL G 286 SHEET 4 AA6 8 VAL G 292 ARG G 298 -1 N CYS G 296 O CYS G 445 SHEET 5 AA6 8 LYS G 328 ASN G 334 -1 O GLU G 332 N ASN G 295 SHEET 6 AA6 8 THR G 413 ILE G 420 -1 O LEU G 416 N CYS G 331 SHEET 7 AA6 8 GLU G 381 CYS G 385 -1 N TYR G 384 O LYS G 419 SHEET 8 AA6 8 HIS G 374 CYS G 378 -1 N HIS G 374 O CYS G 385 SHEET 1 AA7 4 ASP H 3 GLN H 6 0 SHEET 2 AA7 4 GLY H 15 GLN H 25 -1 O GLU H 23 N VAL H 5 SHEET 3 AA7 4 THR H 77 LEU H 82C-1 O LEU H 82C N GLY H 15 SHEET 4 AA7 4 VAL H 67 ASP H 72 -1 N THR H 70 O PHE H 79 SHEET 1 AA8 6 VAL H 10 LYS H 12 0 SHEET 2 AA8 6 THR H 107 ILE H 111 1 O ALA H 108 N VAL H 10 SHEET 3 AA8 6 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA8 6 ILE H 34 ARG H 39 -1 N ARG H 39 O VAL H 89 SHEET 5 AA8 6 GLU H 46 MET H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA8 6 VAL H 57 ASN H 58 -1 O ASN H 58 N TRP H 50 SHEET 1 AA9 4 VAL H 10 LYS H 12 0 SHEET 2 AA9 4 THR H 107 ILE H 111 1 O ALA H 108 N VAL H 10 SHEET 3 AA9 4 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA9 4 LEU H 100K TRP H 103 -1 O LEU H 102 N ARG H 94 SHEET 1 AB1 4 SER H 120 LEU H 124 0 SHEET 2 AB1 4 ALA H 137 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB1 4 TYR H 176 THR H 183 -1 O TYR H 176 N TYR H 145 SHEET 4 AB1 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB2 4 SER H 120 LEU H 124 0 SHEET 2 AB2 4 ALA H 137 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB2 4 TYR H 176 THR H 183 -1 O TYR H 176 N TYR H 145 SHEET 4 AB2 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB3 2 TYR H 194 CYS H 196 0 SHEET 2 AB3 2 LYS H 209 VAL H 211 -1 O LYS H 209 N CYS H 196 SHEET 1 AB4 2 ASN H 199 HIS H 200 0 SHEET 2 AB4 2 THR H 205 LYS H 206 -1 O THR H 205 N HIS H 200 SHEET 1 AB5 5 SER L 9 ALA L 13 0 SHEET 2 AB5 5 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 AB5 5 GLU L 85 ALA L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB5 5 SER L 34 HIS L 38 -1 N HIS L 38 O GLU L 85 SHEET 5 AB5 5 LYS L 45 ILE L 48 -1 O LYS L 45 N GLN L 37 SHEET 1 AB6 4 SER L 9 ALA L 13 0 SHEET 2 AB6 4 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 AB6 4 GLU L 85 ALA L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB6 4 ALA L 97 PHE L 98 -1 O ALA L 97 N ALA L 90 SHEET 1 AB7 3 SER L 18 THR L 24 0 SHEET 2 AB7 3 THR L 70 THR L 76 -1 O LEU L 73 N ILE L 21 SHEET 3 AB7 3 PHE L 62 GLY L 66 -1 N SER L 65 O SER L 72 SHEET 1 AB8 4 SER L 114 LEU L 117 0 SHEET 2 AB8 4 ALA L 130 PHE L 139 -1 O SER L 137 N SER L 114 SHEET 3 AB8 4 TYR L 177 LEU L 180 -1 O LEU L 180 N ALA L 130 SHEET 4 AB8 4 VAL L 159 GLU L 160 -1 N GLU L 160 O TYR L 177 SHEET 1 AB9 4 SER L 114 LEU L 117 0 SHEET 2 AB9 4 ALA L 130 PHE L 139 -1 O SER L 137 N SER L 114 SHEET 3 AB9 4 TYR L 172 ALA L 174 -1 O ALA L 174 N ILE L 136 SHEET 4 AB9 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 173 SHEET 1 AC1 4 SER L 153 VAL L 155 0 SHEET 2 AC1 4 VAL L 144 ALA L 150 -1 N TRP L 148 O VAL L 155 SHEET 3 AC1 4 TYR L 191 HIS L 197 -1 O THR L 196 N THR L 145 SHEET 4 AC1 4 SER L 200 GLU L 203 -1 O SER L 200 N HIS L 197 SSBOND 1 CYS G 54 CYS G 74 1555 1555 2.02 SSBOND 2 CYS G 119 CYS G 205 1555 1555 2.04 SSBOND 3 CYS G 218 CYS G 247 1555 1555 2.69 SSBOND 4 CYS G 228 CYS G 239 1555 1555 2.04 SSBOND 5 CYS G 296 CYS G 331 1555 1555 2.28 SSBOND 6 CYS G 378 CYS G 445 1555 1555 1.91 SSBOND 7 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 8 CYS G 395 CYS G 410 1555 1555 2.04 SSBOND 9 CYS H 140 CYS H 196 1555 1555 2.12 SSBOND 10 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 11 CYS L 134 CYS L 193 1555 1555 2.02 LINK ND2 ASN G 234 C1 NAG G 501 1555 1555 1.45 LINK ND2 ASN G 241 C1 NAG G 502 1555 1555 1.44 LINK ND2 ASN G 262 C1 NAG G 503 1555 1555 1.44 LINK ND2 ASN G 289 C1 NAG G 505 1555 1555 1.46 LINK ND2 ASN G 295 C1 NAG G 506 1555 1555 1.44 LINK ND2 ASN G 334 C1 NAG G 507 1555 1555 1.44 LINK ND2 ASN G 355 C1 NAG G 511 1555 1555 1.46 LINK ND2 ASN G 386 C1 NAG G 508 1555 1555 1.44 LINK ND2 ASN G 392 C1 NAG G 509 1555 1555 1.47 LINK ND2 ASN G 448 C1 NAG G 510 1555 1555 1.43 CISPEP 1 PHE H 146 PRO H 147 0 -9.54 CISPEP 2 GLU H 148 PRO H 149 0 -4.18 CISPEP 3 TYR L 140 PRO L 141 0 -4.22 CRYST1 61.436 63.867 255.285 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 0.016277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003917 0.00000