HEADER VIRAL PROTEIN/ANTIVIRAL PROTEIN 02-JUN-12 3VTQ TITLE NOVEL HIV FUSION INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 3 CHAIN: E, A, B; COMPND 4 FRAGMENT: GP41, UNP RESIDUES 554-589; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FUSION INHIBITOR MT-SIFUVIRTIDE; COMPND 8 CHAIN: D, C, 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 VIRUS; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THE SEQUENCE HAS BEEN DESIGNED KEYWDS 6-HELIX BUNDLE, COILED-COIL, MEMBRANE, FUSION INHIBITOR, M-T HOOK, KEYWDS 2 VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.YAO,S.WALTERSPERGER,M.WANG,S.CUI REVDAT 3 16-OCT-24 3VTQ 1 REMARK REVDAT 2 08-NOV-23 3VTQ 1 SEQADV LINK REVDAT 1 26-JUN-13 3VTQ 0 JRNL AUTH X.YAO,S.WALTERSPERGER,M.WANG,S.CUI JRNL TITL CRYSTAL STRUCTURE OF A NOVEL HIV FUSION INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 34063 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1703 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 36.0981 - 3.5014 0.99 2875 150 0.1965 0.1957 REMARK 3 2 3.5014 - 2.7795 1.00 2769 146 0.1775 0.2178 REMARK 3 3 2.7795 - 2.4282 1.00 2733 144 0.1771 0.1865 REMARK 3 4 2.4282 - 2.2062 0.99 2679 141 0.1966 0.2225 REMARK 3 5 2.2062 - 2.0481 1.00 2696 143 0.1778 0.2309 REMARK 3 6 2.0481 - 1.9274 1.00 2668 140 0.2241 0.2388 REMARK 3 7 1.9274 - 1.8309 0.98 2642 139 0.2733 0.3105 REMARK 3 8 1.8309 - 1.7512 1.00 2669 141 0.2057 0.2481 REMARK 3 9 1.7512 - 1.6837 1.00 2680 141 0.2039 0.2215 REMARK 3 10 1.6837 - 1.6256 1.00 2673 141 0.2023 0.2517 REMARK 3 11 1.6256 - 1.5748 1.00 2679 141 0.2172 0.2503 REMARK 3 12 1.5748 - 1.5298 0.98 2597 136 0.2269 0.2357 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 34.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.530 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) : -4.30620 REMARK 3 B22 (A**2) : 7.13440 REMARK 3 B33 (A**2) : -2.82820 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.006 2000 REMARK 3 ANGLE : 0.826 2711 REMARK 3 CHIRALITY : 0.048 294 REMARK 3 PLANARITY : 0.003 358 REMARK 3 DIHEDRAL : 14.784 797 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 3VTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000095488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : 34063 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 36.088 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.330 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 17.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : 0.46300 REMARK 200 FOR SHELL : 4.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER MR REMARK 200 STARTING MODEL: 3VIE REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.14M CALCIUM CHLORIDE, 0.1M SODIUM REMARK 280 ACETATE, 18 %(V/V) ISOPROPANOL, PH 4.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.99500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.94550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.92900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.94550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.99500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.92900 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: 12530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, A, B, D, C, 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 NH2 E 71 REMARK 465 NH2 A 71 REMARK 465 NH2 B 71 REMARK 465 NH2 D 152 REMARK 465 NH2 C 152 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 HH22 ARG C 144 O HOH C 227 1.43 REMARK 500 O HOH A 110 O HOH A 121 1.97 REMARK 500 O HOH D 206 O HOH D 211 1.98 REMARK 500 O HOH E 111 O HOH E 116 2.02 REMARK 500 O HOH A 119 O HOH A 120 2.07 REMARK 500 O HOH B 123 O HOH B 128 2.10 REMARK 500 OE1 GLN D 130 O HOH D 231 2.10 REMARK 500 O HOH E 129 O HOH E 132 2.11 REMARK 500 O HOH E 117 O HOH C 230 2.13 REMARK 500 NH2 ARG C 144 O HOH C 227 2.14 REMARK 500 O HOH C 231 O HOH C 233 2.15 REMARK 500 OE1 GLU D 151 O HOH D 239 2.16 REMARK 500 O HOH F 229 O HOH F 235 2.17 REMARK 500 O HOH E 129 O HOH D 229 2.18 REMARK 500 OE1 GLN E 39 O HOH E 115 2.18 REMARK 500 OE1 GLN A 40 O HOH A 102 2.18 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 NH2 ARG F 122 O HOH C 213 1455 2.10 REMARK 500 NE2 GLN A 39 OE2 GLU D 137 3645 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VIE RELATED DB: PDB REMARK 900 RELATED ID: 3VGX RELATED DB: PDB REMARK 900 RELATED ID: 3VTP RELATED DB: PDB DBREF 3VTQ E 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VTQ A 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VTQ B 35 70 UNP Q9YP39 Q9YP39_9HIV1 554 589 DBREF 3VTQ D 114 152 PDB 3VTQ 3VTQ 114 152 DBREF 3VTQ C 114 152 PDB 3VTQ 3VTQ 114 152 DBREF 3VTQ F 114 152 PDB 3VTQ 3VTQ 114 152 SEQADV 3VTQ ACE E 34 UNP Q9YP39 ACETYLATION SEQADV 3VTQ NH2 E 71 UNP Q9YP39 AMIDATION SEQADV 3VTQ ACE A 34 UNP Q9YP39 ACETYLATION SEQADV 3VTQ NH2 A 71 UNP Q9YP39 AMIDATION SEQADV 3VTQ ACE B 34 UNP Q9YP39 ACETYLATION SEQADV 3VTQ NH2 B 71 UNP Q9YP39 AMIDATION SEQRES 1 E 38 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 E 38 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 E 38 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU NH2 SEQRES 1 A 38 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 A 38 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 A 38 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU NH2 SEQRES 1 B 38 ACE SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 B 38 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 B 38 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU NH2 SEQRES 1 D 39 ACE MET THR TRP GLU THR TRP GLU ARG GLU ILE GLU ASN SEQRES 2 D 39 TYR THR LYS GLN ILE TYR LYS ILE LEU GLU GLU SER GLN SEQRES 3 D 39 GLU GLN GLN ASP ARG ASN GLU LYS ASP LEU LEU GLU NH2 SEQRES 1 C 39 ACE MET THR TRP GLU THR TRP GLU ARG GLU ILE GLU ASN SEQRES 2 C 39 TYR THR LYS GLN ILE TYR LYS ILE LEU GLU GLU SER GLN SEQRES 3 C 39 GLU GLN GLN ASP ARG ASN GLU LYS ASP LEU LEU GLU NH2 SEQRES 1 F 39 ACE MET THR TRP GLU THR TRP GLU ARG GLU ILE GLU ASN SEQRES 2 F 39 TYR THR LYS GLN ILE TYR LYS ILE LEU GLU GLU SER GLN SEQRES 3 F 39 GLU GLN GLN ASP ARG ASN GLU LYS ASP LEU LEU GLU NH2 HET ACE E 34 3 HET ACE A 34 3 HET ACE B 34 3 HET ACE D 114 3 HET ACE C 114 3 HET ACE F 114 3 HET NH2 F 152 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 6(C2 H4 O) FORMUL 6 NH2 H2 N FORMUL 7 HOH *197(H2 O) HELIX 1 1 SER E 35 LEU E 70 1 36 HELIX 2 2 SER A 35 LEU A 70 1 36 HELIX 3 3 SER B 35 LEU B 70 1 36 HELIX 4 4 THR D 116 GLU D 151 1 36 HELIX 5 5 THR C 116 LEU C 149 1 34 HELIX 6 6 THR F 116 GLU F 151 1 36 LINK C ACE E 34 N SER E 35 1555 1555 1.33 LINK C ACE A 34 N SER A 35 1555 1555 1.33 LINK C ACE B 34 N SER B 35 1555 1555 1.33 LINK C ACE D 114 N MET D 115 1555 1555 1.33 LINK C ACE C 114 N MET C 115 1555 1555 1.33 LINK C ACE F 114 N MET F 115 1555 1555 1.33 LINK C GLU F 151 N NH2 F 152 1555 1555 1.33 CRYST1 41.990 47.858 109.891 90.00 90.00 90.00 P 21 21 21 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 0.023815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009100 0.00000 HETATM 1 C ACE E 34 35.094 5.192 25.062 1.00 31.57 C HETATM 2 O ACE E 34 34.005 5.355 24.510 1.00 24.05 O HETATM 3 CH3 ACE E 34 35.277 5.533 26.537 1.00 38.64 C