HEADER SUGAR BINDING PROTEIN 21-FEB-18 5ZCX TITLE STRUCTURE OF T20/N39 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: N39; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 8 CHAIN: W, P, Q; COMPND 9 SYNONYM: T20; COMPND 10 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 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 8 ORGANISM_TAXID: 11676 KEYWDS 6-HB, HELICES, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.J.ZHANG,X.H.DING REVDAT 2 19-DEC-18 5ZCX 1 COMPND JRNL REVDAT 1 10-OCT-18 5ZCX 0 JRNL AUTH X.ZHANG,X.DING,Y.ZHU,H.CHONG,S.CUI,J.HE,X.WANG,Y.HE JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF HIV-1 CELL JRNL TITL 2 FUSION INHIBITOR T20. JRNL REF AIDS V. 33 1 2019 JRNL REFN ISSN 1473-5571 JRNL PMID 30096076 JRNL DOI 10.1097/QAD.0000000000001979 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 37.5402 - 3.3152 0.99 3132 158 0.2230 0.2328 REMARK 3 2 3.3152 - 2.6316 1.00 3073 153 0.2630 0.2973 REMARK 3 3 2.6316 - 2.2990 1.00 3039 164 0.2273 0.2483 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.930 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.010 1477 REMARK 3 ANGLE : 0.910 1991 REMARK 3 CHIRALITY : 0.037 239 REMARK 3 PLANARITY : 0.005 261 REMARK 3 DIHEDRAL : 15.936 917 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 5ZCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300005746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9725 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.299 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CAESIUM CHLORIDE 0.1 M MES PH REMARK 280 6.5 30 % V/V JEFFAMINE M-600, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K 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 19.00050 REMARK 290 SMTRY3 2 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: 9640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, W, P, Q, C 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 SER A 17 REMARK 465 THR A 18 REMARK 465 MET A 19 REMARK 465 GLY A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 SER A 23 REMARK 465 MET A 24 REMARK 465 SER B 17 REMARK 465 THR B 18 REMARK 465 MET B 19 REMARK 465 GLY B 20 REMARK 465 ALA B 21 REMARK 465 ALA B 22 REMARK 465 SER B 23 REMARK 465 MET B 24 REMARK 465 THR B 25 REMARK 465 LEU B 26 REMARK 465 THR B 27 REMARK 465 VAL B 28 REMARK 465 ASN W 160 REMARK 465 TRP W 161 REMARK 465 PHE W 162 REMARK 465 ACE P 126 REMARK 465 ALA P 156 REMARK 465 SER P 157 REMARK 465 LEU P 158 REMARK 465 TRP P 159 REMARK 465 ASN P 160 REMARK 465 TRP P 161 REMARK 465 PHE P 162 REMARK 465 TRP Q 159 REMARK 465 ASN Q 160 REMARK 465 TRP Q 161 REMARK 465 PHE Q 162 REMARK 465 SER C 17 REMARK 465 THR C 18 REMARK 465 MET C 19 REMARK 465 GLY C 20 REMARK 465 ALA C 21 REMARK 465 ALA C 22 REMARK 465 SER C 23 REMARK 465 MET C 24 REMARK 465 THR C 25 REMARK 465 LEU C 26 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN B 29 CG CD OE1 NE2 REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 32 CG CD OE1 NE2 REMARK 470 ARG B 46 CG CD NE CZ NH1 NH2 REMARK 470 GLU W 143 CG CD OE1 OE2 REMARK 470 TRP W 155 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP W 155 CZ3 CH2 REMARK 470 TRP W 159 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP W 159 CZ3 CH2 REMARK 470 SER P 133 OG REMARK 470 GLU P 137 CG CD OE1 OE2 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 HE21 GLN A 51 OE1 GLN C 52 1.47 REMARK 500 HE21 GLN W 141 O HOH W 201 1.59 REMARK 500 HD22 ASN Q 145 O HOH Q 201 1.59 REMARK 500 OE1 GLN C 51 O HOH C 101 1.96 REMARK 500 NE2 GLN B 52 O HOH B 101 2.16 REMARK 500 O LEU B 54 O HOH B 102 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 TRP W 155 -2.25 -57.55 REMARK 500 ALA W 156 -63.38 -108.86 REMARK 500 LYS Q 154 -75.57 -62.00 REMARK 500 SER Q 157 28.91 -79.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 5ZCX A 17 55 UNP C4MJC7 C4MJC7_9HIV1 49 87 DBREF 5ZCX B 17 55 UNP C4MJC7 C4MJC7_9HIV1 49 87 DBREF 5ZCX W 127 162 UNP Q6TAQ3 Q6TAQ3_9HIV1 634 669 DBREF 5ZCX P 127 162 UNP Q6TAQ3 Q6TAQ3_9HIV1 634 669 DBREF 5ZCX Q 127 162 UNP Q6TAQ3 Q6TAQ3_9HIV1 634 669 DBREF 5ZCX C 17 55 UNP C4MJC7 C4MJC7_9HIV1 49 87 SEQADV 5ZCX ACE W 126 UNP Q6TAQ3 ACETYLATION SEQADV 5ZCX ACE P 126 UNP Q6TAQ3 ACETYLATION SEQADV 5ZCX ACE Q 126 UNP Q6TAQ3 ACETYLATION SEQRES 1 A 39 SER THR MET GLY ALA ALA SER MET THR LEU THR VAL GLN SEQRES 2 A 39 ALA ARG GLN LEU LEU SER GLY ILE VAL GLN GLN GLN ASN SEQRES 3 A 39 ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU SEQRES 1 B 39 SER THR MET GLY ALA ALA SER MET THR LEU THR VAL GLN SEQRES 2 B 39 ALA ARG GLN LEU LEU SER GLY ILE VAL GLN GLN GLN ASN SEQRES 3 B 39 ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU SEQRES 1 W 37 ACE TYR THR SER LEU ILE HIS SER LEU ILE GLU GLU SER SEQRES 2 W 37 GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU SEQRES 3 W 37 LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE SEQRES 1 P 37 ACE TYR THR SER LEU ILE HIS SER LEU ILE GLU GLU SER SEQRES 2 P 37 GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU SEQRES 3 P 37 LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE SEQRES 1 Q 37 ACE TYR THR SER LEU ILE HIS SER LEU ILE GLU GLU SER SEQRES 2 Q 37 GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU SEQRES 3 Q 37 LEU ASP LYS TRP ALA SER LEU TRP ASN TRP PHE SEQRES 1 C 39 SER THR MET GLY ALA ALA SER MET THR LEU THR VAL GLN SEQRES 2 C 39 ALA ARG GLN LEU LEU SER GLY ILE VAL GLN GLN GLN ASN SEQRES 3 C 39 ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU HET ACE W 126 3 HET ACE Q 126 3 HETNAM ACE ACETYL GROUP FORMUL 3 ACE 2(C2 H4 O) FORMUL 7 HOH *18(H2 O) HELIX 1 AA1 THR A 25 LEU A 55 1 31 HELIX 2 AA2 ALA B 30 LEU B 55 1 26 HELIX 3 AA3 TYR W 127 LEU W 158 1 32 HELIX 4 AA4 THR P 128 LYS P 154 1 27 HELIX 5 AA5 TYR Q 127 SER Q 157 1 31 HELIX 6 AA6 VAL C 28 LEU C 55 1 28 LINK C ACE W 126 N TYR W 127 1555 1555 1.33 LINK C ACE Q 126 N TYR Q 127 1555 1555 1.32 CRYST1 39.790 38.001 73.080 90.00 101.52 90.00 P 1 21 1 6 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 0.025132 0.000000 0.005124 0.00000 SCALE2 0.000000 0.026315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013965 0.00000