HEADER VIRAL PROTEIN/TRANSCRIPTION INHIBITOR 23-FEB-12 4DVV TITLE CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX TITLE 2 WITH AS-I-261 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, AS-I-261, KEYWDS 2 VIRAL PROTEIN-TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,P.D.KWONG REVDAT 5 13-SEP-23 4DVV 1 HETSYN REVDAT 4 29-JUL-20 4DVV 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 31-MAY-17 4DVV 1 COMPND REMARK DBREF REVDAT 2 19-MAR-14 4DVV 1 JRNL REVDAT 1 27-FEB-13 4DVV 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. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 58216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2944 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 26.3926 - 5.3355 0.96 2742 143 0.1755 0.1982 REMARK 3 2 5.3355 - 4.2406 0.99 2779 139 0.1454 0.1691 REMARK 3 3 4.2406 - 3.7062 0.99 2750 157 0.1584 0.1938 REMARK 3 4 3.7062 - 3.3681 0.99 2722 151 0.1679 0.1957 REMARK 3 5 3.3681 - 3.1271 1.00 2718 165 0.1802 0.1952 REMARK 3 6 3.1271 - 2.9430 1.00 2773 125 0.1890 0.2638 REMARK 3 7 2.9430 - 2.7958 1.00 2781 134 0.1922 0.2372 REMARK 3 8 2.7958 - 2.6742 1.00 2735 164 0.2013 0.2270 REMARK 3 9 2.6742 - 2.5713 1.00 2747 147 0.1958 0.2497 REMARK 3 10 2.5713 - 2.4827 1.00 2722 142 0.2063 0.2521 REMARK 3 11 2.4827 - 2.4051 0.99 2709 152 0.2164 0.2669 REMARK 3 12 2.4051 - 2.3364 1.00 2771 150 0.2022 0.2664 REMARK 3 13 2.3364 - 2.2749 1.00 2729 137 0.2043 0.2346 REMARK 3 14 2.2749 - 2.2194 0.99 2710 166 0.1969 0.2379 REMARK 3 15 2.2194 - 2.1690 0.99 2736 139 0.2075 0.2204 REMARK 3 16 2.1690 - 2.1229 0.99 2668 147 0.2166 0.2948 REMARK 3 17 2.1229 - 2.0804 0.97 2690 123 0.2262 0.2955 REMARK 3 18 2.0804 - 2.0412 0.93 2544 127 0.2301 0.2669 REMARK 3 19 2.0412 - 2.0047 0.88 2386 119 0.2419 0.2796 REMARK 3 20 2.0047 - 1.9708 0.77 2131 128 0.2474 0.2671 REMARK 3 21 1.9708 - 1.9390 0.63 1729 89 0.2567 0.2844 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.72190 REMARK 3 B22 (A**2) : 1.62990 REMARK 3 B33 (A**2) : -5.35180 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.70810 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 5842 REMARK 3 ANGLE : 0.856 7930 REMARK 3 CHIRALITY : 0.052 924 REMARK 3 PLANARITY : 0.003 980 REMARK 3 DIHEDRAL : 14.703 2206 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): 18.2107 2.4257 39.4033 REMARK 3 T TENSOR REMARK 3 T11: 0.1487 T22: 0.1933 REMARK 3 T33: 0.2332 T12: 0.0213 REMARK 3 T13: 0.0199 T23: -0.0417 REMARK 3 L TENSOR REMARK 3 L11: 2.3874 L22: 3.6924 REMARK 3 L33: 2.4380 L12: -0.2340 REMARK 3 L13: 0.6482 L23: -0.9478 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: 0.0399 S13: 0.1906 REMARK 3 S21: 0.0446 S22: -0.0533 S23: -0.1085 REMARK 3 S31: -0.2156 S32: -0.0639 S33: 0.0899 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): 14.8099 -19.8309 40.7424 REMARK 3 T TENSOR REMARK 3 T11: 0.1626 T22: 0.2136 REMARK 3 T33: 0.2318 T12: 0.0078 REMARK 3 T13: 0.0462 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 2.2799 L22: 2.1352 REMARK 3 L33: 2.4518 L12: -0.3927 REMARK 3 L13: 1.5948 L23: -0.1787 REMARK 3 S TENSOR REMARK 3 S11: 0.0511 S12: -0.2098 S13: -0.1740 REMARK 3 S21: -0.0090 S22: -0.0048 S23: -0.0025 REMARK 3 S31: 0.2510 S32: -0.1475 S33: -0.0336 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): -12.5470 -16.4137 9.2509 REMARK 3 T TENSOR REMARK 3 T11: 0.4929 T22: 0.2893 REMARK 3 T33: 0.2876 T12: 0.0164 REMARK 3 T13: -0.0890 T23: 0.0658 REMARK 3 L TENSOR REMARK 3 L11: 4.5836 L22: 3.8394 REMARK 3 L33: 3.0149 L12: -1.4761 REMARK 3 L13: -0.5244 L23: -0.5702 REMARK 3 S TENSOR REMARK 3 S11: 0.0737 S12: 0.0669 S13: 0.2065 REMARK 3 S21: -0.3214 S22: 0.1093 S23: 0.3269 REMARK 3 S31: -0.1121 S32: -0.5421 S33: -0.1598 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0075 -38.6985 12.0232 REMARK 3 T TENSOR REMARK 3 T11: 0.7291 T22: 0.2973 REMARK 3 T33: 0.4761 T12: -0.1523 REMARK 3 T13: -0.1510 T23: 0.0984 REMARK 3 L TENSOR REMARK 3 L11: 4.1004 L22: 3.4448 REMARK 3 L33: 2.3675 L12: -1.5706 REMARK 3 L13: -0.4968 L23: 0.0352 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.1404 S13: -0.9324 REMARK 3 S21: -0.3903 S22: 0.2183 S23: 0.6662 REMARK 3 S31: 0.7638 S32: -0.4674 S33: -0.0907 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 4DVV 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_1000070847. 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 : 58230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 26.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 FOR SHELL : 2.230 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 (%): 53.68 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, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 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 34.03950 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 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 OE2 GLU A 83 O HOH A 725 1.85 REMARK 500 O HOH A 641 O HOH A 816 1.92 REMARK 500 O HOH A 790 O HOH A 791 1.92 REMARK 500 O HOH A 810 O HOH A 848 1.93 REMARK 500 NE ARG A 480 O HOH A 789 1.94 REMARK 500 O HOH B 695 O HOH B 696 1.97 REMARK 500 O HOH B 667 O HOH B 672 1.97 REMARK 500 OE1 GLU A 293 O HOH A 766 2.00 REMARK 500 O HOH A 667 O HOH A 827 2.02 REMARK 500 O HOH B 690 O HOH B 691 2.02 REMARK 500 O HOH A 815 O HOH A 835 2.03 REMARK 500 O LYS A 240 O HOH A 690 2.04 REMARK 500 O HOH A 807 O HOH A 818 2.05 REMARK 500 ND2 ASN A 334 C2 NAG A 507 2.07 REMARK 500 O HOH A 647 O HOH A 713 2.08 REMARK 500 ND2 ASN B 289 C2 NAG B 505 2.09 REMARK 500 O HOH A 809 O HOH A 812 2.11 REMARK 500 O HOH B 689 O HOH B 711 2.11 REMARK 500 ND2 ASN A 411 O HOH A 829 2.12 REMARK 500 N GLY A 324 O HOH A 839 2.13 REMARK 500 ND2 ASN B 448 C2 NAG B 511 2.13 REMARK 500 O HOH A 814 O HOH A 817 2.13 REMARK 500 O HOH A 744 O HOH A 823 2.13 REMARK 500 O THR A 123 OG SER A 199 2.14 REMARK 500 O HOH A 819 O HOH A 847 2.14 REMARK 500 O HOH A 800 O HOH A 804 2.14 REMARK 500 O HOH B 664 O HOH B 678 2.15 REMARK 500 N ASN A 411 O HOH A 816 2.17 REMARK 500 ND2 ASN B 386 C2 NAG B 509 2.18 REMARK 500 O HOH A 796 O HOH A 847 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 NZ LYS B 202 O HOH B 702 2545 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 ASN A 88 16.24 58.42 REMARK 500 LEU A 116 53.52 -118.36 REMARK 500 ASP A 211 104.61 -166.88 REMARK 500 GLN A 258 -63.89 67.16 REMARK 500 GLU A 268 -96.05 -112.13 REMARK 500 ASN A 276 94.48 -167.26 REMARK 500 CYS A 395 30.73 -88.85 REMARK 500 LEU B 116 62.91 -111.78 REMARK 500 ASP B 211 108.73 -164.32 REMARK 500 GLN B 258 -62.44 64.91 REMARK 500 GLU B 268 -96.53 -127.52 REMARK 500 ASN B 355 -1.59 57.39 REMARK 500 THR B 358 126.06 -35.68 REMARK 500 PHE B 391 60.75 -111.19 REMARK 500 ALA B 460 28.79 -164.79 REMARK 500 ASN B 462 5.04 83.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 782 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH A 838 DISTANCE = 5.81 ANGSTROMS 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: 4DVW 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 4DVV A 44 492 UNP A0A0M3KKW9_9HIV1 DBREF2 4DVV A A0A0M3KKW9 1 353 DBREF1 4DVV B 44 492 UNP A0A0M3KKW9_9HIV1 DBREF2 4DVV B A0A0M3KKW9 1 353 SEQADV 4DVV SER A 375 UNP A0A0M3KKW HIS 242 ENGINEERED MUTATION SEQADV 4DVV 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 4DVV ASN B 241 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 355 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 448 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 355 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 448 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 392 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 392 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 234 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 262 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 334 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 234 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 386 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 295 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 334 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 276 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 386 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 241 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 289 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 295 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 262 ASN GLYCOSYLATION SITE MODRES 4DVV ASN A 289 ASN GLYCOSYLATION SITE MODRES 4DVV ASN B 276 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 NAG A 511 14 HET EPE A 512 15 HET 0M1 A 513 24 HET NAG B 501 14 HET NAG B 502 14 HET NAG B 503 14 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 NAG B 511 14 HET EPE B 512 15 HET 0M1 B 513 24 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM 0M1 N-{[(4S,5S)-5-(AMINOMETHYL)-2,2-DIMETHYL-1,3-DIOXOLAN- HETNAM 2 0M1 4-YL]METHYL}-N'-(4-CHLORO-3-FLUOROPHENYL)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 22(C8 H15 N O6) FORMUL 14 EPE 2(C8 H18 N2 O4 S) FORMUL 15 0M1 2(C15 H19 CL F N3 O4) FORMUL 29 HOH *378(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 ILE A 475 TYR A 484 1 10 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 PHE B 353 1 19 HELIX 10 10 ASP B 368 MET B 373 1 6 HELIX 11 11 ASN B 392 ILE B 396 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 HIS A 85 -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 CYS A 54 O VAL A 75 SHEET 3 B 3 HIS A 216 CYS A 218 -1 O HIS A 216 N ALA A 55 SHEET 1 C 2 GLU A 91 ASN A 94 0 SHEET 2 C 2 THR A 236 CYS A 239 -1 O CYS A 239 N GLU A 91 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 ILE A 414 N ILE A 333 SHEET 6 F 7 GLU A 381 CYS A 385 -1 N PHE A 382 O LYS A 421 SHEET 7 F 7 HIS A 374 CYS A 378 -1 N PHE A 376 O PHE A 383 SHEET 1 G 5 TRP B 45 ASP B 47 0 SHEET 2 G 5 TYR B 486 ILE B 491 -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 VAL B 245 N ILE B 225 SHEET 5 G 5 ILE B 84 HIS B 85 -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 CYS B 54 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 GLU B 466 PRO B 470 0 SHEET 5 K 5 ILE B 359 PHE B 361 1 N ILE B 360 O GLU B 466 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 HIS B 374 O CYS B 385 SSBOND 1 CYS A 54 CYS A 74 1555 1555 2.03 SSBOND 2 CYS A 119 CYS A 205 1555 1555 2.03 SSBOND 3 CYS A 218 CYS A 247 1555 1555 2.04 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 2.04 SSBOND 9 CYS B 119 CYS B 205 1555 1555 2.03 SSBOND 10 CYS B 218 CYS B 247 1555 1555 2.04 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 1.45 LINK ND2 ASN A 276 C1 NAG A 504 1555 1555 1.44 LINK ND2 ASN A 289 C1 NAG A 505 1555 1555 1.45 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 1.44 LINK ND2 ASN A 386 C1 NAG A 509 1555 1555 1.44 LINK ND2 ASN A 392 C1 NAG A 510 1555 1555 1.44 LINK ND2 ASN A 448 C1 NAG A 511 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 1.45 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 392 C1 NAG B 510 1555 1555 1.44 LINK ND2 ASN B 448 C1 NAG B 511 1555 1555 1.44 CRYST1 64.779 68.079 94.350 90.00 91.42 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 0.015437 0.000000 0.000383 0.00000 SCALE2 0.000000 0.014689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010602 0.00000