HEADER VIRAL PROTEIN 22-MAY-07 2JPR TITLE JOINT REFINEMENT OF THE HIV-1 CA-NTD IN COMPLEX WITH THE ASSEMBLY TITLE 2 INHIBITOR CAP-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES, 133-277; COMPND 5 SYNONYM: PR160GAG-POL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (NEW YORK-5 SOURCE 3 ISOLATE); SOURCE 4 ORGANISM_TAXID: 11698; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLN4-3 KEYWDS CAP-1, CAPSID, HIV-1, ASSEMBLY INHIBITOR, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.N.KELLY,S.KYERE,I.KINDE,C.TANG,B.R.HOWARD,H.ROBINSON,W.I.SUNDQUIST, AUTHOR 2 M.F.SUMMERS,C.P.HILL REVDAT 4 29-MAY-24 2JPR 1 REMARK REVDAT 3 09-MAR-22 2JPR 1 REMARK REVDAT 2 24-FEB-09 2JPR 1 VERSN REVDAT 1 09-OCT-07 2JPR 0 JRNL AUTH B.N.KELLY,S.KYERE,I.KINDE,C.TANG,B.R.HOWARD,H.ROBINSON, JRNL AUTH 2 W.I.SUNDQUIST,M.F.SUMMERS,C.P.HILL JRNL TITL STRUCTURE OF THE ANTIVIRAL ASSEMBLY INHIBITOR CAP-1 COMPLEX JRNL TITL 2 WITH THE HIV-1 CA PROTEIN JRNL REF J.MOL.BIOL. V. 373 355 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17826792 JRNL DOI 10.1016/J.JMB.2007.07.070 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE OF THE "BOUND" CONFORMATION OF THE HIV-1 CAPSID REMARK 3 PROTEIN (IN THE REMARK 3 PRESENCE OF THE LIGAND) WAS OBTAINED FROM THE CRYSTAL. THE REMARK 3 COMPLEX WAS REMARK 3 CALCULATED USING NMR DISTANCE RESTRAINTS IN REFERENCE TO THE BOUND REMARK 3 CONFORMATION OF THE CAPSID PROTEIN. REFINEMENT WAS PERFORMED REMARK 3 USING SIMULATED REMARK 3 MOLECULAR DYNAMICS IN AMBER 9.0. REMARK 4 REMARK 4 2JPR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000100135. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100-700 UM [U-15N] SODIUM REMARK 210 PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 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 1 TYR A 145 C TYR A 145 OXT 0.648 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 7 ARG A 100 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PXR RELATED DB: PDB REMARK 900 HIV-1 CA146 IN THE PRESENCE OF CAP-1 REMARK 900 RELATED ID: 2PWM RELATED DB: PDB REMARK 900 HIV-1 CA146 A92E REAL CELL REMARK 900 RELATED ID: 2PWO RELATED DB: PDB REMARK 900 HIV-1 CA146 A92E PSUEDO CELL DBREF 2JPR A 1 145 UNP P12497 POL_HV1N5 133 277 SEQRES 1 A 145 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 A 145 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 A 145 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 A 145 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 A 145 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 A 145 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 A 145 GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 A 145 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 A 145 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 A 145 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 A 145 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 A 145 MET TYR HET JPR A 146 50 HETNAM JPR 1-(3-CHLORO-4-METHYLPHENYL)-3-{2-[({5-[(DIMETHYLAMINO) HETNAM 2 JPR METHYL]-2-FURYL}METHYL)THIO]ETHYL}UREA FORMUL 2 JPR C18 H24 CL N3 O2 S HELIX 1 1 SER A 16 ALA A 31 1 16 HELIX 2 2 GLU A 35 LEU A 43 1 9 HELIX 3 3 THR A 48 THR A 58 1 11 HELIX 4 4 HIS A 62 HIS A 84 1 23 HELIX 5 5 ARG A 100 ALA A 105 1 6 HELIX 6 6 THR A 110 THR A 119 1 10 HELIX 7 7 PRO A 125 TYR A 145 1 21 SHEET 1 A 2 ILE A 2 GLN A 4 0 SHEET 2 A 2 MET A 10 HIS A 12 -1 O VAL A 11 N VAL A 3 CISPEP 1 ASN A 121 PRO A 122 1 -6.59 CISPEP 2 ASN A 121 PRO A 122 2 -6.77 CISPEP 3 ASN A 121 PRO A 122 3 -6.61 CISPEP 4 ASN A 121 PRO A 122 4 -6.64 CISPEP 5 ASN A 121 PRO A 122 5 -6.60 CISPEP 6 ASN A 121 PRO A 122 6 -6.66 CISPEP 7 ASN A 121 PRO A 122 7 -6.58 CISPEP 8 ASN A 121 PRO A 122 8 -6.68 CISPEP 9 ASN A 121 PRO A 122 9 -6.68 CISPEP 10 ASN A 121 PRO A 122 10 -6.64 CISPEP 11 ASN A 121 PRO A 122 11 -6.62 CISPEP 12 ASN A 121 PRO A 122 12 -6.62 CISPEP 13 ASN A 121 PRO A 122 13 -6.62 CISPEP 14 ASN A 121 PRO A 122 14 -6.64 CISPEP 15 ASN A 121 PRO A 122 15 -6.68 CISPEP 16 ASN A 121 PRO A 122 16 -6.60 CISPEP 17 ASN A 121 PRO A 122 17 -6.64 CISPEP 18 ASN A 121 PRO A 122 18 -6.65 CISPEP 19 ASN A 121 PRO A 122 19 -6.65 CISPEP 20 ASN A 121 PRO A 122 20 -6.69 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1