HEADER VIRAL PROTEIN/TRANSCRIPTION INHIBITOR 23-FEB-12 4DVW TITLE CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX TITLE 2 WITH MAE-II-167 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLADE A/E 93TH057 HIV-1 GP120 CORE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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: 293F; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PVRC8400 KEYWDS HIV-1 GP120, SMALL MOLECULE INHIBITOR, CD4 BINDING SITE, MAE-II-167, KEYWDS 2 VIRAL PROTEIN-TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,P.D.KWONG REVDAT 5 13-SEP-23 4DVW 1 HETSYN REVDAT 4 29-JUL-20 4DVW 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 31-MAY-17 4DVW 1 COMPND REMARK DBREF REVDAT 2 19-MAR-14 4DVW 1 JRNL REVDAT 1 27-FEB-13 4DVW 0 JRNL AUTH Y.D.KWON,J.M.LALONDE,Y.YANG,M.A.ELBAN,A.SUGAWARA, JRNL AUTH 2 J.R.COURTER,D.M.JONES,A.B.SMITH,A.K.DEBNATH,P.D.KWONG JRNL TITL CRYSTAL STRUCTURES OF HIV-1 GP120 ENVELOPE GLYCOPROTEIN IN JRNL TITL 2 COMPLEX WITH NBD ANALOGUES THAT TARGET THE CD4-BINDING SITE. JRNL REF PLOS ONE V. 9 85940 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24489681 JRNL DOI 10.1371/JOURNAL.PONE.0085940 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 39980 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 27.7415 - 5.2673 0.99 2957 150 0.1787 0.2434 REMARK 3 2 5.2673 - 4.1855 0.99 2902 151 0.1525 0.1983 REMARK 3 3 4.1855 - 3.6577 0.98 2840 157 0.1672 0.1934 REMARK 3 4 3.6577 - 3.3239 0.98 2856 139 0.1815 0.2204 REMARK 3 5 3.3239 - 3.0860 0.99 2846 156 0.1938 0.2326 REMARK 3 6 3.0860 - 2.9043 0.99 2854 154 0.1984 0.2508 REMARK 3 7 2.9043 - 2.7589 0.99 2833 140 0.2054 0.2533 REMARK 3 8 2.7589 - 2.6389 0.98 2815 150 0.2044 0.2755 REMARK 3 9 2.6389 - 2.5374 0.98 2783 161 0.2090 0.2639 REMARK 3 10 2.5374 - 2.4499 0.96 2786 137 0.2125 0.2625 REMARK 3 11 2.4499 - 2.3734 0.93 2677 135 0.2246 0.2516 REMARK 3 12 2.3734 - 2.3056 0.90 2542 149 0.2231 0.2772 REMARK 3 13 2.3056 - 2.2449 0.82 2359 120 0.2363 0.3218 REMARK 3 14 2.2449 - 2.1901 0.67 1924 107 0.2475 0.2878 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.39290 REMARK 3 B22 (A**2) : 0.52000 REMARK 3 B33 (A**2) : -6.91290 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.08100 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 : 0.002 5811 REMARK 3 ANGLE : 0.521 7886 REMARK 3 CHIRALITY : 0.034 915 REMARK 3 PLANARITY : 0.002 978 REMARK 3 DIHEDRAL : 11.998 2186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 1:252 OR RESID 474:492) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2687 2.4974 39.3487 REMARK 3 T TENSOR REMARK 3 T11: 0.1882 T22: 0.2198 REMARK 3 T33: 0.2771 T12: -0.0038 REMARK 3 T13: 0.0296 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 2.6453 L22: 3.5863 REMARK 3 L33: 3.0171 L12: -0.4796 REMARK 3 L13: 1.0333 L23: -0.8751 REMARK 3 S TENSOR REMARK 3 S11: -0.0543 S12: 0.0267 S13: 0.2427 REMARK 3 S21: 0.0488 S22: -0.0806 S23: 0.0005 REMARK 3 S31: -0.2915 S32: -0.0838 S33: 0.1065 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): 14.8954 -19.8112 40.7309 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.2370 REMARK 3 T33: 0.2758 T12: 0.0153 REMARK 3 T13: 0.0589 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 2.2110 L22: 2.0541 REMARK 3 L33: 3.4133 L12: -0.3252 REMARK 3 L13: 1.9815 L23: -0.4033 REMARK 3 S TENSOR REMARK 3 S11: 0.0275 S12: -0.1834 S13: -0.1368 REMARK 3 S21: 0.0332 S22: -0.0318 S23: 0.0044 REMARK 3 S31: 0.2733 S32: -0.1041 S33: -0.0093 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESID 1:252 OR RESID 474:492) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4127 -16.3857 9.2280 REMARK 3 T TENSOR REMARK 3 T11: 0.4949 T22: 0.3058 REMARK 3 T33: 0.3286 T12: 0.0282 REMARK 3 T13: -0.0803 T23: 0.0719 REMARK 3 L TENSOR REMARK 3 L11: 5.3767 L22: 3.4971 REMARK 3 L33: 3.3274 L12: -1.3951 REMARK 3 L13: -0.9618 L23: -0.1584 REMARK 3 S TENSOR REMARK 3 S11: 0.0930 S12: 0.0942 S13: 0.2665 REMARK 3 S21: -0.2529 S22: 0.0519 S23: 0.2927 REMARK 3 S31: -0.1566 S32: -0.4761 S33: -0.1113 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): -10.9850 -38.6429 12.0497 REMARK 3 T TENSOR REMARK 3 T11: 0.7341 T22: 0.3404 REMARK 3 T33: 0.5401 T12: -0.1272 REMARK 3 T13: -0.1130 T23: 0.0871 REMARK 3 L TENSOR REMARK 3 L11: 4.0532 L22: 2.8045 REMARK 3 L33: 2.8538 L12: -1.0476 REMARK 3 L13: -0.6433 L23: 0.4108 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: -0.0928 S13: -0.8375 REMARK 3 S21: -0.1800 S22: 0.1431 S23: 0.5830 REMARK 3 S31: 0.7396 S32: -0.4754 S33: -0.0511 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 4DVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35700 REMARK 200 R SYM FOR SHELL (I) : 0.40200 REMARK 200 FOR SHELL : 2.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3TGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 5% ISO-PROPANOL, 0.1M REMARK 280 HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH REMARK 280 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.26650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: MONOMER 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 318 REMARK 465 GLY A 319 REMARK 465 SER A 320 REMARK 465 GLY A 321 REMARK 465 SER A 322 REMARK 465 GLY A 323 REMARK 465 GLY A 403 REMARK 465 ASN A 404 REMARK 465 GLU A 405 REMARK 465 THR A 406 REMARK 465 MET A 407 REMARK 465 LYS A 408 REMARK 465 GLY A 409 REMARK 465 CYS A 410 REMARK 465 GLY B 318 REMARK 465 GLY B 319 REMARK 465 SER B 320 REMARK 465 GLY B 321 REMARK 465 SER B 322 REMARK 465 GLY B 323 REMARK 465 GLY B 403 REMARK 465 ASN B 404 REMARK 465 GLU B 405 REMARK 465 THR B 406 REMARK 465 MET B 407 REMARK 465 LYS B 408 REMARK 465 GLY B 409 REMARK 465 CYS B 410 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 B 633 O HOH B 638 1.85 REMARK 500 O HOH A 731 O HOH A 733 1.86 REMARK 500 ND2 ASN A 334 O HOH A 750 1.94 REMARK 500 OE1 GLU B 106 O HOH B 652 1.94 REMARK 500 ND2 ASN B 448 C2 NAG B 510 1.96 REMARK 500 O HOH A 736 O HOH A 739 1.96 REMARK 500 N ILE B 201 O HOH B 657 1.97 REMARK 500 N ASN B 461 O HOH B 667 1.99 REMARK 500 O HOH A 719 O HOH A 729 2.03 REMARK 500 O HOH B 673 O HOH B 679 2.03 REMARK 500 O HOH A 704 O HOH A 711 2.05 REMARK 500 O3 NAG A 503 O HOH A 655 2.05 REMARK 500 NE ARG A 480 O HOH A 744 2.07 REMARK 500 ND2 ASN A 334 C2 NAG A 507 2.07 REMARK 500 O HOH A 691 O HOH A 708 2.09 REMARK 500 O HOH A 619 O HOH A 674 2.09 REMARK 500 O HOH A 605 O HOH A 706 2.09 REMARK 500 ND2 ASN A 289 C2 NAG A 505 2.11 REMARK 500 OD1 ASN A 411 O HOH A 722 2.12 REMARK 500 ND2 ASN A 355 C2 NAG A 508 2.12 REMARK 500 N ASN B 462 O HOH B 667 2.12 REMARK 500 OE2 GLU A 62 O HOH A 720 2.13 REMARK 500 O HOH A 725 O HOH A 737 2.16 REMARK 500 OG1 THR B 358 O SER B 464 2.16 REMARK 500 ND2 ASN B 289 C2 NAG B 505 2.18 REMARK 500 ND2 ASN B 386 C2 NAG B 509 2.18 REMARK 500 NZ LYS A 59 O HOH A 741 2.19 REMARK 500 O5 NAG B 509 O HOH B 659 2.19 REMARK 500 OD1 ASP A 457 O HOH A 664 2.19 REMARK 500 O THR A 236 O HOH A 694 2.19 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 A 211 105.39 -170.01 REMARK 500 GLN A 258 -63.99 68.79 REMARK 500 GLU A 268 -101.88 -109.86 REMARK 500 SER A 274 140.28 -172.26 REMARK 500 ASN A 276 94.29 -171.46 REMARK 500 PHE A 391 54.50 -113.36 REMARK 500 CYS A 395 40.56 -85.90 REMARK 500 TRP B 45 164.17 51.21 REMARK 500 ASN B 94 88.44 -153.43 REMARK 500 LEU B 116 69.57 -104.47 REMARK 500 THR B 123 -109.10 -107.48 REMARK 500 ASP B 211 103.37 -163.31 REMARK 500 GLN B 258 -63.14 63.14 REMARK 500 GLU B 268 -103.20 -123.12 REMARK 500 ASN B 276 89.48 -174.71 REMARK 500 ASP B 325 110.67 75.71 REMARK 500 ASN B 354 56.29 31.79 REMARK 500 ASN B 355 25.34 49.86 REMARK 500 SER B 365 -70.47 -66.18 REMARK 500 ASN B 392 -27.74 -162.95 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 B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DVR RELATED DB: PDB REMARK 900 RELATED ID: 4DVS RELATED DB: PDB REMARK 900 RELATED ID: 4DVT RELATED DB: PDB REMARK 900 RELATED ID: 4DVU RELATED DB: PDB REMARK 900 RELATED ID: 4DVV RELATED DB: PDB REMARK 900 RELATED ID: 4DVX RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL REMARK 999 1-43, BY REPLACING THE V1/V2 REGIONS WITH A GG LINKER, AND REMARK 999 REPLACING V3 REGION WITH A LINKER GGSGSG DBREF1 4DVW A 44 492 UNP A0A0M3KKW9_9HIV1 DBREF2 4DVW A A0A0M3KKW9 1 353 DBREF1 4DVW B 44 492 UNP A0A0M3KKW9_9HIV1 DBREF2 4DVW B A0A0M3KKW9 1 353 SEQADV 4DVW SER A 375 UNP A0A0M3KKW HIS 242 ENGINEERED MUTATION SEQADV 4DVW SER B 375 UNP A0A0M3KKW HIS 242 ENGINEERED MUTATION SEQRES 1 A 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 A 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 A 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 A 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 A 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 A 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 A 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 A 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 A 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 A 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 A 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 A 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 A 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 A 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 A 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 A 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 A 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 A 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 A 353 ASP LEU GLU ILE THR MET HIS SER PHE ASN CYS ARG GLY SEQRES 20 A 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 A 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 A 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 A 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 A 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 A 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 A 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 A 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 A 353 ILE GLU SEQRES 1 B 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 B 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 B 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 B 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 B 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 B 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 B 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 B 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 B 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 B 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 B 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 B 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 B 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 B 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 B 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 B 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 B 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 B 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 B 353 ASP LEU GLU ILE THR MET HIS SER PHE ASN CYS ARG GLY SEQRES 20 B 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 B 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 B 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 B 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 B 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 B 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 B 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 B 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 B 353 ILE GLU MODRES 4DVW ASN A 355 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 295 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 386 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 234 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 234 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 241 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 386 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 295 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 448 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 241 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 289 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 276 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 334 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 448 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 262 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 276 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 334 ASN GLYCOSYLATION SITE MODRES 4DVW ASN B 355 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 289 ASN GLYCOSYLATION SITE MODRES 4DVW ASN A 262 ASN GLYCOSYLATION SITE HET NAG A 501 14 HET NAG A 502 14 HET NAG A 503 14 HET NAG A 504 14 HET NAG A 505 14 HET NAG A 506 14 HET NAG A 507 14 HET NAG A 508 14 HET NAG A 509 14 HET NAG A 510 14 HET EPE A 511 15 HET 0M4 A 512 42 HET NAG B 501 14 HET NAG B 502 14 HET NAG B 503 13 HET NAG B 504 14 HET NAG B 505 14 HET NAG B 506 14 HET NAG B 507 14 HET NAG B 508 14 HET NAG B 509 14 HET NAG B 510 14 HET EPE B 511 15 HET 0M4 B 512 42 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM 0M4 N-(4-CHLORO-3-FLUOROPHENYL)-N'-[(3AS,6AS)- HETNAM 2 0M4 HEXAHYDROCYCLOPENTA[C]PYRROL-3A(1H)- HETNAM 3 0M4 YLMETHYL]ETHANEDIAMIDE 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 HETSYN EPE HEPES FORMUL 3 NAG 20(C8 H15 N O6) FORMUL 13 EPE 2(C8 H18 N2 O4 S) FORMUL 14 0M4 2(C16 H19 CL F N3 O2) FORMUL 27 HOH *231(H2 O) HELIX 1 1 GLU A 64 CYS A 74 1 11 HELIX 2 2 ASN A 98 LEU A 116 1 19 HELIX 3 3 GLY A 335 PHE A 353 1 19 HELIX 4 4 ASP A 368 MET A 373 1 6 HELIX 5 5 ASN A 392 ILE A 396 5 5 HELIX 6 6 ASN A 474 TYR A 484 1 11 HELIX 7 7 GLU B 64 ALA B 73 1 10 HELIX 8 8 ASN B 98 LEU B 116 1 19 HELIX 9 9 GLY B 335 HIS B 352 1 18 HELIX 10 10 ASP B 368 MET B 373 1 6 HELIX 11 11 THR B 387 PHE B 391 5 5 HELIX 12 12 ILE B 475 TYR B 484 1 10 SHEET 1 A 5 TRP A 45 ASP A 47 0 SHEET 2 A 5 TYR A 486 ILE A 491 -1 O GLN A 490 N LYS A 46 SHEET 3 A 5 TYR A 223 CYS A 228 -1 N LEU A 226 O LYS A 487 SHEET 4 A 5 VAL A 242 VAL A 245 -1 O SER A 243 N LYS A 227 SHEET 5 A 5 GLU A 83 LEU A 86 -1 N ILE A 84 O SER A 244 SHEET 1 B 3 VAL A 75 PRO A 76 0 SHEET 2 B 3 PHE A 53 SER A 56 1 N SER A 56 O VAL A 75 SHEET 3 B 3 HIS A 216 CYS A 218 -1 O CYS A 218 N PHE A 53 SHEET 1 C 2 GLU A 91 ASN A 94 0 SHEET 2 C 2 THR A 236 CYS A 239 -1 O GLY A 237 N PHE A 93 SHEET 1 D 4 SER A 199 LYS A 202 0 SHEET 2 D 4 VAL A 120 THR A 123 -1 N LYS A 121 O ILE A 201 SHEET 3 D 4 GLN A 432 MET A 434 -1 O GLN A 432 N LEU A 122 SHEET 4 D 4 ILE A 423 ASN A 425 -1 N ILE A 424 O ALA A 433 SHEET 1 E 5 LEU A 259 LEU A 261 0 SHEET 2 E 5 ILE A 443 ARG A 456 -1 O GLY A 451 N LEU A 260 SHEET 3 E 5 ILE A 284 ARG A 298 -1 N VAL A 286 O ILE A 452 SHEET 4 E 5 ASN A 465 PRO A 470 0 SHEET 5 E 5 THR A 358 PHE A 361 1 N ILE A 360 O PHE A 468 SHEET 1 F 7 ILE A 271 ARG A 273 0 SHEET 2 F 7 ILE A 284 ARG A 298 -1 O HIS A 287 N ILE A 271 SHEET 3 F 7 ILE A 443 ARG A 456 -1 O ILE A 452 N VAL A 286 SHEET 4 F 7 LYS A 328 ASN A 334 0 SHEET 5 F 7 THR A 413 LYS A 421 -1 O LEU A 416 N CYS A 331 SHEET 6 F 7 GLU A 381 CYS A 385 -1 N TYR A 384 O LYS A 419 SHEET 7 F 7 HIS A 374 CYS A 378 -1 N PHE A 376 O PHE A 383 SHEET 1 G 5 LYS B 46 ASP B 47 0 SHEET 2 G 5 TYR B 486 GLN B 490 -1 O GLN B 490 N LYS B 46 SHEET 3 G 5 TYR B 223 CYS B 228 -1 N LEU B 226 O LYS B 487 SHEET 4 G 5 VAL B 242 VAL B 245 -1 O SER B 243 N LYS B 227 SHEET 5 G 5 ILE B 84 LEU B 86 -1 N ILE B 84 O SER B 244 SHEET 1 H 3 CYS B 74 PRO B 76 0 SHEET 2 H 3 PHE B 53 SER B 56 1 N SER B 56 O VAL B 75 SHEET 3 H 3 HIS B 216 CYS B 218 -1 O CYS B 218 N PHE B 53 SHEET 1 I 2 GLU B 91 ASN B 94 0 SHEET 2 I 2 THR B 236 CYS B 239 -1 O GLY B 237 N PHE B 93 SHEET 1 J 4 VAL B 200 LYS B 202 0 SHEET 2 J 4 VAL B 120 LEU B 122 -1 N LYS B 121 O ILE B 201 SHEET 3 J 4 GLN B 432 MET B 434 -1 O GLN B 432 N LEU B 122 SHEET 4 J 4 ILE B 423 ASN B 425 -1 N ILE B 424 O ALA B 433 SHEET 1 K 5 LEU B 259 LEU B 261 0 SHEET 2 K 5 ILE B 443 ARG B 456 -1 O GLY B 451 N LEU B 260 SHEET 3 K 5 ILE B 284 ARG B 298 -1 N VAL B 286 O ILE B 452 SHEET 4 K 5 ASN B 465 PRO B 470 0 SHEET 5 K 5 THR B 358 PHE B 361 1 N ILE B 360 O PHE B 468 SHEET 1 L 7 ILE B 271 ARG B 273 0 SHEET 2 L 7 ILE B 284 ARG B 298 -1 O HIS B 287 N ILE B 271 SHEET 3 L 7 ILE B 443 ARG B 456 -1 O ILE B 452 N VAL B 286 SHEET 4 L 7 LYS B 328 ASN B 334 0 SHEET 5 L 7 THR B 413 ILE B 420 -1 O LEU B 416 N CYS B 331 SHEET 6 L 7 GLU B 381 CYS B 385 -1 N TYR B 384 O LYS B 419 SHEET 7 L 7 HIS B 374 CYS B 378 -1 N CYS B 378 O GLU B 381 SSBOND 1 CYS A 54 CYS A 74 1555 1555 2.04 SSBOND 2 CYS A 119 CYS A 205 1555 1555 2.03 SSBOND 3 CYS A 218 CYS A 247 1555 1555 2.03 SSBOND 4 CYS A 228 CYS A 239 1555 1555 2.04 SSBOND 5 CYS A 296 CYS A 331 1555 1555 2.03 SSBOND 6 CYS A 378 CYS A 445 1555 1555 2.03 SSBOND 7 CYS A 385 CYS A 418 1555 1555 2.03 SSBOND 8 CYS B 54 CYS B 74 1555 1555 2.03 SSBOND 9 CYS B 119 CYS B 205 1555 1555 2.03 SSBOND 10 CYS B 218 CYS B 247 1555 1555 2.03 SSBOND 11 CYS B 228 CYS B 239 1555 1555 2.03 SSBOND 12 CYS B 296 CYS B 331 1555 1555 2.03 SSBOND 13 CYS B 378 CYS B 445 1555 1555 2.03 SSBOND 14 CYS B 385 CYS B 418 1555 1555 2.03 LINK ND2 ASN A 234 C1 NAG A 501 1555 1555 1.44 LINK ND2 ASN A 241 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN A 262 C1 NAG A 503 1555 1555 1.44 LINK ND2 ASN A 276 C1 NAG A 504 1555 1555 1.44 LINK ND2 ASN A 289 C1 NAG A 505 1555 1555 1.44 LINK ND2 ASN A 295 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 334 C1 NAG A 507 1555 1555 1.44 LINK ND2 ASN A 355 C1 NAG A 508 1555 1555 1.43 LINK ND2 ASN A 386 C1 NAG A 509 1555 1555 1.44 LINK ND2 ASN A 448 C1 NAG A 510 1555 1555 1.44 LINK ND2 ASN B 234 C1 NAG B 501 1555 1555 1.44 LINK ND2 ASN B 241 C1 NAG B 502 1555 1555 1.44 LINK ND2 ASN B 262 C1 NAG B 503 1555 1555 1.44 LINK ND2 ASN B 276 C1 NAG B 504 1555 1555 1.44 LINK ND2 ASN B 289 C1 NAG B 505 1555 1555 1.44 LINK ND2 ASN B 295 C1 NAG B 506 1555 1555 1.44 LINK ND2 ASN B 334 C1 NAG B 507 1555 1555 1.44 LINK ND2 ASN B 355 C1 NAG B 508 1555 1555 1.44 LINK ND2 ASN B 386 C1 NAG B 509 1555 1555 1.44 LINK ND2 ASN B 448 C1 NAG B 510 1555 1555 1.44 CRYST1 64.591 68.533 94.155 90.00 91.27 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015482 0.000000 0.000343 0.00000 SCALE2 0.000000 0.014592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010623 0.00000