HEADER VIRAL PROTEIN/ANTIVIRAL PROTEIN 29-SEP-11 3VIE TITLE HIV-GP41 FUSION INHIBITOR SIFUVIRTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 3 CHAIN: A, C, E; COMPND 4 FRAGMENT: NHR DOMAIN, UNP RESIDUES 554-589; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SIFUVIRTIDE; COMPND 8 CHAIN: B, D, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 OTHER_DETAILS: NHR 35-70 SEQUENCE OCCURS NATURALLY IN HIV-1; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: SEQUENCE OF SIFUVIRTIDE HAS BEEN DESIGNED BASED ON SOURCE 9 SEQUENCE OF HIV-1 GP41 CHR KEYWDS 6-HELIX BUNDLE, MEMBRANE FUSION INHIBITION, HIV, VIRAL PROTEIN- KEYWDS 2 ANTIVIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.YAO,S.WALTERSPERGER,M.T.WANG,S.CUI REVDAT 5 20-NOV-24 3VIE 1 REMARK REVDAT 4 08-NOV-23 3VIE 1 SEQADV LINK REVDAT 3 24-JUL-13 3VIE 1 JRNL REVDAT 2 29-FEB-12 3VIE 1 TITLE REVDAT 1 18-JAN-12 3VIE 0 JRNL AUTH X.YAO,H.CHONG,C.ZHANG,S.WALTERSPERGER,M.WANG,S.CUI,Y.HE JRNL TITL BROAD ANTIVIRAL ACTIVITY AND CRYSTAL STRUCTURE OF HIV-1 JRNL TITL 2 FUSION INHIBITOR SIFUVIRTIDE JRNL REF J.BIOL.CHEM. V. 287 6788 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22228771 JRNL DOI 10.1074/JBC.M111.317883 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.810 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 22201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1109 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 34.9425 - 3.5989 0.99 2702 140 0.2122 0.2139 REMARK 3 2 3.5989 - 2.8570 1.00 2685 142 0.1585 0.2025 REMARK 3 3 2.8570 - 2.4960 1.00 2671 140 0.1687 0.2062 REMARK 3 4 2.4960 - 2.2678 1.00 2667 141 0.1560 0.2398 REMARK 3 5 2.2678 - 2.1053 1.00 2637 138 0.1571 0.2170 REMARK 3 6 2.1053 - 1.9812 1.00 2662 141 0.1675 0.2434 REMARK 3 7 1.9812 - 1.8820 1.00 2633 138 0.1846 0.2250 REMARK 3 8 1.8820 - 1.8000 0.92 2435 129 0.2010 0.2576 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 : 0.46 REMARK 3 B_SOL : 64.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.74080 REMARK 3 B22 (A**2) : 6.67260 REMARK 3 B33 (A**2) : -7.41340 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.85350 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 : 0.018 2210 REMARK 3 ANGLE : 1.490 3016 REMARK 3 CHIRALITY : 0.117 312 REMARK 3 PLANARITY : 0.006 410 REMARK 3 DIHEDRAL : 16.919 926 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3VIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000095082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR CRYSTAL REMARK 200 TYPE SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XDS PACKAGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.701 REMARK 200 RESOLUTION RANGE LOW (A) : 44.391 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 3.180 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.24 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.510 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: PDB ENTRY 1ENV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS HCL, 10% W/V PEG 4000, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.39350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.58950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.39350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.58950 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E, B, D, F 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 LEU A 70 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TRP D 117 CA CB CG CD1 CD2 NE1 CE2 REMARK 480 TRP D 117 CE3 CZ2 CZ3 CH2 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 ACE B 115 HA SER B 116 1.47 REMARK 500 CH3 ACE F 115 N SER F 116 1.67 REMARK 500 O HOH A 12 O HOH A 13 2.01 REMARK 500 OE1 GLU B 123 O HOH B 53 2.05 REMARK 500 OE1 GLN C 56 O HOH C 91 2.06 REMARK 500 O HOH C 83 O HOH C 84 2.15 REMARK 500 O HOH C 72 O HOH B 78 2.19 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 SER B 116 C - N - CA ANGL. DEV. = -34.9 DEGREES REMARK 500 ACE D 115 O - C - N ANGL. DEV. = 15.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 3VIE A 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VIE C 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VIE E 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VIE B 115 151 PDB 3VIE 3VIE 115 151 DBREF 3VIE D 115 151 PDB 3VIE 3VIE 115 151 DBREF 3VIE F 115 151 PDB 3VIE 3VIE 115 151 SEQADV 3VIE ACE A 34 UNP Q9YP39 ACETYLATION SEQADV 3VIE ACE C 34 UNP Q9YP39 ACETYLATION SEQADV 3VIE ACE E 34 UNP Q9YP39 ACETYLATION SEQRES 1 A 37 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 A 37 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 A 37 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SEQRES 1 C 37 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 C 37 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 C 37 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SEQRES 1 E 37 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 E 37 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 E 37 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SEQRES 1 B 37 ACE SER TRP GLU THR TRP GLU ARG GLU ILE GLU ASN TYR SEQRES 2 B 37 THR ARG GLN ILE TYR ARG ILE LEU GLU GLU SER GLN GLU SEQRES 3 B 37 GLN GLN ASP ARG ASN GLU ARG ASP LEU LEU GLU SEQRES 1 D 37 ACE SER TRP GLU THR TRP GLU ARG GLU ILE GLU ASN TYR SEQRES 2 D 37 THR ARG GLN ILE TYR ARG ILE LEU GLU GLU SER GLN GLU SEQRES 3 D 37 GLN GLN ASP ARG ASN GLU ARG ASP LEU LEU GLU SEQRES 1 F 37 ACE SER TRP GLU THR TRP GLU ARG GLU ILE GLU ASN TYR SEQRES 2 F 37 THR ARG GLN ILE TYR ARG ILE LEU GLU GLU SER GLN GLU SEQRES 3 F 37 GLN GLN ASP ARG ASN GLU ARG ASP LEU LEU GLU HET ACE A 34 3 HET ACE C 34 3 HET ACE E 34 3 HET ACE B 115 3 HET ACE D 115 3 HET ACE F 115 3 HETNAM ACE ACETYL GROUP FORMUL 1 ACE 6(C2 H4 O) FORMUL 7 HOH *93(H2 O) HELIX 1 1 SER A 35 ILE A 69 1 35 HELIX 2 2 SER C 35 LEU C 70 1 36 HELIX 3 3 SER E 35 LEU E 70 1 36 HELIX 4 4 SER B 116 GLU B 151 1 36 HELIX 5 5 SER D 116 GLU D 151 1 36 HELIX 6 6 SER F 116 LEU F 150 1 35 LINK C ACE A 34 N SER A 35 1555 1555 1.33 LINK C ACE C 34 N SER C 35 1555 1555 1.33 LINK C ACE E 34 N SER E 35 1555 1555 1.33 LINK C ACE B 115 N SER B 116 1555 1555 1.36 LINK C ACE D 115 N SER D 116 1555 1555 1.34 LINK C ACE F 115 N SER F 116 1555 1555 1.20 CRYST1 88.787 49.179 55.818 90.00 90.65 90.00 C 1 2 1 12 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 0.011263 0.000000 0.000128 0.00000 SCALE2 0.000000 0.020334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017917 0.00000 HETATM 1 C ACE A 34 -10.593 11.049 17.664 1.00 25.43 C HETATM 2 O ACE A 34 -10.648 11.193 16.439 1.00 27.02 O HETATM 3 CH3 ACE A 34 -11.650 11.672 18.511 1.00 25.21 C