HEADER HYDROLASE 04-FEB-12 4DKV TITLE CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX TITLE 2 WITH NBD-10007 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 GP120 CORE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CHIMERA RESIDUES 44-492; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: CLADE A/E 93TH057; SOURCE 5 GENE: ENV; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PVRC8400 KEYWDS HIV-1 GP120, CLADE A/E, CD4 MIMIC, NBD-10007, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,A.K.DEBNATH,P.D.KWONG REVDAT 5 13-SEP-23 4DKV 1 REMARK REVDAT 4 19-MAY-21 4DKV 1 SOURCE HETSYN REVDAT 3 29-JUL-20 4DKV 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 02-AUG-17 4DKV 1 SOURCE JRNL REVDAT 1 20-MAR-13 4DKV 0 JRNL AUTH F.CURRELI,Y.D.KWON,H.ZHANG,Y.YANG,D.SCACALOSSI,P.D.KWONG, JRNL AUTH 2 A.K.DEBNATH JRNL TITL BINDING MODE CHARACTERIZATION OF NBD SERIES CD4-MIMETIC JRNL TITL 2 HIV-1 ENTRY INHIBITORS BY X-RAY STRUCTURE AND RESISTANCE JRNL TITL 3 STUDY. JRNL REF ANTIMICROB. AGENTS V. 58 5478 2014 JRNL REF 2 CHEMOTHER. JRNL REFN ESSN 1098-6596 JRNL PMID 25001301 JRNL DOI 10.1128/AAC.03339-14 REMARK 2 REMARK 2 RESOLUTION. 2.18 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 39018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1954 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 27.6040 - 5.2542 0.99 2965 146 0.1908 0.2171 REMARK 3 2 5.2542 - 4.1750 0.99 2896 161 0.1671 0.1918 REMARK 3 3 4.1750 - 3.6486 0.99 2862 142 0.1804 0.2032 REMARK 3 4 3.6486 - 3.3157 0.99 2871 145 0.1947 0.2247 REMARK 3 5 3.3157 - 3.0783 0.99 2879 149 0.2068 0.2522 REMARK 3 6 3.0783 - 2.8970 1.00 2888 145 0.2191 0.2627 REMARK 3 7 2.8970 - 2.7521 1.00 2875 155 0.2187 0.2867 REMARK 3 8 2.7521 - 2.6324 1.00 2888 141 0.2257 0.2785 REMARK 3 9 2.6324 - 2.5311 1.00 2831 174 0.2286 0.2637 REMARK 3 10 2.5311 - 2.4438 0.99 2862 157 0.2461 0.3394 REMARK 3 11 2.4438 - 2.3675 0.94 2710 141 0.2598 0.3102 REMARK 3 12 2.3675 - 2.2998 0.82 2310 123 0.2634 0.3052 REMARK 3 13 2.2998 - 2.2393 0.65 1877 99 0.2773 0.3175 REMARK 3 14 2.2393 - 2.1847 0.47 1350 76 0.2919 0.3000 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24860 REMARK 3 B22 (A**2) : 3.94580 REMARK 3 B33 (A**2) : -3.69720 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.77370 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 : 0.008 5824 REMARK 3 ANGLE : 0.965 7900 REMARK 3 CHIRALITY : 0.047 916 REMARK 3 PLANARITY : 0.003 980 REMARK 3 DIHEDRAL : 13.919 2190 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): 17.7466 2.5158 39.2129 REMARK 3 T TENSOR REMARK 3 T11: 0.1722 T22: 0.1923 REMARK 3 T33: 0.2821 T12: 0.0048 REMARK 3 T13: 0.0615 T23: -0.0353 REMARK 3 L TENSOR REMARK 3 L11: 3.7591 L22: 4.0309 REMARK 3 L33: 4.8565 L12: -0.7291 REMARK 3 L13: 1.9158 L23: -1.2629 REMARK 3 S TENSOR REMARK 3 S11: -0.0426 S12: 0.0388 S13: 0.3577 REMARK 3 S21: 0.0287 S22: -0.0916 S23: -0.0800 REMARK 3 S31: -0.2734 S32: -0.0441 S33: 0.1397 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6414 -19.7943 40.6439 REMARK 3 T TENSOR REMARK 3 T11: 0.2226 T22: 0.2497 REMARK 3 T33: 0.3177 T12: -0.0012 REMARK 3 T13: 0.0900 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 3.1114 L22: 1.6342 REMARK 3 L33: 5.7579 L12: -0.3119 REMARK 3 L13: 3.9285 L23: -0.1494 REMARK 3 S TENSOR REMARK 3 S11: 0.0686 S12: -0.2492 S13: -0.1546 REMARK 3 S21: 0.0635 S22: -0.0476 S23: 0.0714 REMARK 3 S31: 0.4026 S32: -0.2454 S33: -0.0174 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): -12.4419 -16.5151 9.1436 REMARK 3 T TENSOR REMARK 3 T11: 0.4299 T22: 0.2729 REMARK 3 T33: 0.2404 T12: -0.0004 REMARK 3 T13: -0.0681 T23: 0.0911 REMARK 3 L TENSOR REMARK 3 L11: 8.3765 L22: 4.2646 REMARK 3 L33: 4.0324 L12: -1.3569 REMARK 3 L13: -1.8499 L23: -0.1146 REMARK 3 S TENSOR REMARK 3 S11: 0.0338 S12: 0.1845 S13: 0.2211 REMARK 3 S21: -0.2247 S22: 0.0985 S23: 0.3054 REMARK 3 S31: -0.0286 S32: -0.6065 S33: -0.1058 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0370 -38.8008 11.8389 REMARK 3 T TENSOR REMARK 3 T11: 0.7410 T22: 0.3824 REMARK 3 T33: 0.4735 T12: -0.1741 REMARK 3 T13: -0.1414 T23: 0.0832 REMARK 3 L TENSOR REMARK 3 L11: 7.1175 L22: 3.0455 REMARK 3 L33: 2.5023 L12: -0.6472 REMARK 3 L13: -1.0635 L23: 0.4185 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: 0.2318 S13: -0.9605 REMARK 3 S21: -0.3601 S22: 0.1345 S23: 0.5373 REMARK 3 S31: 0.8990 S32: -0.5679 S33: -0.1079 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 4DKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070456. 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) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.185 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 (%) : 92.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.51800 REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 FOR SHELL : 1.320 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 (%): 53.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 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 34.38650 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 O HOH B 670 O HOH B 672 1.81 REMARK 500 O GLY B 472 O HOH B 651 1.83 REMARK 500 O3 NAG A 503 O HOH A 664 1.84 REMARK 500 OD1 ASN A 280 O HOH A 714 1.86 REMARK 500 N ASN B 474 O HOH B 651 1.87 REMARK 500 ND2 ASN B 411 O HOH B 659 1.89 REMARK 500 OE2 GLU B 269 O HOH B 678 1.92 REMARK 500 CG ASN B 411 O HOH B 659 1.93 REMARK 500 OE2 GLU B 293 O HOH B 663 1.93 REMARK 500 N ASN B 411 O HOH B 659 1.96 REMARK 500 O HOH A 703 O HOH A 713 2.00 REMARK 500 O HOH A 672 O HOH A 677 2.01 REMARK 500 NH2 ARG A 480 O HOH A 663 2.04 REMARK 500 N ASN B 411 O HOH B 664 2.06 REMARK 500 O GLN B 117 O HOH B 640 2.11 REMARK 500 O HOH A 674 O HOH A 675 2.14 REMARK 500 OE1 GLN B 114 O HOH B 642 2.16 REMARK 500 O LYS B 59 O HOH B 602 2.17 REMARK 500 ND2 ASN A 289 C2 NAG A 505 2.17 REMARK 500 CA ASN B 411 O HOH B 664 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 238 CD PRO A 238 N 0.086 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 80 69.31 -119.12 REMARK 500 ASP A 211 104.79 -166.53 REMARK 500 GLN A 258 -63.88 62.95 REMARK 500 GLU A 268 -102.36 -97.39 REMARK 500 ASN A 276 95.81 -166.86 REMARK 500 SER A 300 -76.19 -73.08 REMARK 500 PHE A 391 64.50 -110.27 REMARK 500 CYS A 395 49.23 -85.25 REMARK 500 THR A 430 -76.40 -71.88 REMARK 500 LEU B 116 62.62 -108.43 REMARK 500 ASP B 211 104.01 -161.75 REMARK 500 GLN B 258 -66.32 59.41 REMARK 500 GLU B 268 -101.66 -125.09 REMARK 500 ASN B 276 95.76 -172.71 REMARK 500 ASN B 355 73.70 38.96 REMARK 500 PHE B 391 51.43 -109.23 REMARK 500 ASN B 393 31.37 -76.46 REMARK 500 CYS B 395 59.06 -102.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKU RELATED DB: PDB DBREF 4DKV A 44 123 UNP Q0ED31 Q0ED31_9HIV1 43 122 DBREF 4DKV A 199 301 UNP Q0ED31 Q0ED31_9HIV1 201 303 DBREF 4DKV A 324 492 UNP Q0ED31 Q0ED31_9HIV1 325 486 DBREF 4DKV B 44 123 UNP Q0ED31 Q0ED31_9HIV1 43 122 DBREF 4DKV B 199 301 UNP Q0ED31 Q0ED31_9HIV1 201 303 DBREF 4DKV B 324 492 UNP Q0ED31 Q0ED31_9HIV1 325 486 SEQADV 4DKV GLY A 124 UNP Q0ED31 LINKER SEQADV 4DKV GLY A 198 UNP Q0ED31 LINKER SEQADV 4DKV GLY A 318 UNP Q0ED31 LINKER SEQADV 4DKV GLY A 319 UNP Q0ED31 LINKER SEQADV 4DKV SER A 320 UNP Q0ED31 LINKER SEQADV 4DKV GLY A 321 UNP Q0ED31 LINKER SEQADV 4DKV SER A 322 UNP Q0ED31 LINKER SEQADV 4DKV GLY A 323 UNP Q0ED31 LINKER SEQADV 4DKV SER A 375 UNP Q0ED31 HIS 375 ENGINEERED MUTATION SEQADV 4DKV GLY B 124 UNP Q0ED31 LINKER SEQADV 4DKV GLY B 198 UNP Q0ED31 LINKER SEQADV 4DKV GLY B 318 UNP Q0ED31 LINKER SEQADV 4DKV GLY B 319 UNP Q0ED31 LINKER SEQADV 4DKV SER B 320 UNP Q0ED31 LINKER SEQADV 4DKV GLY B 321 UNP Q0ED31 LINKER SEQADV 4DKV SER B 322 UNP Q0ED31 LINKER SEQADV 4DKV GLY B 323 UNP Q0ED31 LINKER SEQADV 4DKV SER B 375 UNP Q0ED31 HIS 375 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 4DKV ASN A 241 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 448 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 262 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 386 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 234 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 334 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 386 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 392 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 289 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 234 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 262 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 334 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 448 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 295 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 295 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 355 ASN GLYCOSYLATION SITE MODRES 4DKV ASN A 276 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 241 ASN GLYCOSYLATION SITE MODRES 4DKV ASN B 289 ASN GLYCOSYLATION SITE MODRES 4DKV 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 0KW A 513 54 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 EPE B 510 15 HET 0KW B 511 54 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM 0KW N-(4-CHLOROPHENYL)-N'-{(S)-[5-(2-HYDROXYETHYL)-4- HETNAM 2 0KW METHYL-1,3-THIAZOL-2-YL][(2S)-PIPERIDIN-2- HETNAM 3 0KW YL]METHYL}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 14 EPE 2(C8 H18 N2 O4 S) FORMUL 15 0KW 2(C20 H25 CL N4 O3 S) FORMUL 27 HOH *196(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 GLU B 351 1 17 HELIX 10 10 ASP B 368 MET B 373 1 6 HELIX 11 11 ASN B 474 TYR B 484 1 11 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 VAL A 245 N ILE A 225 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 ILE A 420 -1 O ILE A 414 N ILE A 333 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 CYS A 378 O GLU A 381 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 SER B 243 N LYS B 227 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 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 ILE B 201 LYS B 202 0 SHEET 2 J 4 VAL B 120 LYS B 121 -1 N LYS B 121 O ILE B 201 SHEET 3 J 4 GLN B 432 MET B 434 -1 O MET B 434 N VAL B 120 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 ILE B 285 N ARG B 273 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 ILE B 414 N ILE B 333 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 2.03 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 2.20 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 1.42 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 1.43 LINK ND2 ASN A 295 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 334 C1 NAG A 507 1555 1555 1.43 LINK ND2 ASN A 355 C1 NAG A 508 1555 1555 1.44 LINK ND2 ASN A 386 C1 NAG A 509 1555 1555 1.43 LINK ND2 ASN A 392 C1 NAG A 510 1555 1555 1.43 LINK ND2 ASN A 448 C1 NAG A 511 1555 1555 1.44 LINK ND2 ASN B 234 C1 NAG B 501 1555 1555 1.43 LINK ND2 ASN B 241 C1 NAG B 502 1555 1555 1.45 LINK ND2 ASN B 262 C1 NAG B 503 1555 1555 1.43 LINK ND2 ASN B 276 C1 NAG B 504 1555 1555 1.53 LINK ND2 ASN B 289 C1 NAG B 505 1555 1555 1.48 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 386 C1 NAG B 508 1555 1555 1.43 LINK ND2 ASN B 448 C1 NAG B 509 1555 1555 1.42 CRYST1 64.333 68.773 93.848 90.00 91.74 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 0.015544 0.000000 0.000472 0.00000 SCALE2 0.000000 0.014541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010660 0.00000