HEADER VIRAL PROTEIN 27-JUL-98 1BMX TITLE HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MAJOR HOMOLOGY REGION PEPTIDE, N-TERMINAL CYS; COMPND 5 SYNONYM: HIV-1 P24 MHR PEPTIDE ANALOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV, VIRAL CAPSID, P24, MHR, MAJOR HOMOLOGY REGION, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR C.B.CLISH,D.H.PEYTON,E.BARKLIS REVDAT 4 16-FEB-22 1BMX 1 REMARK SEQADV REVDAT 3 24-FEB-09 1BMX 1 VERSN REVDAT 2 16-FEB-99 1BMX 3 ATOM HET SOURCE COMPND REVDAT 2 2 3 REMARK TITLE HETATM FORMUL REVDAT 2 3 3 KEYWDS HEADER TER CONECT REVDAT 2 4 3 HETNAM LINK REVDAT 1 06-JAN-99 1BMX 0 JRNL AUTH C.B.CLISH,D.H.PEYTON,E.BARKLIS JRNL TITL SOLUTION STRUCTURES OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 JRNL TITL 2 (HIV-1) AND MOLONEY MURINE LEUKEMIA VIRUS (MOMLV) CAPSID JRNL TITL 3 PROTEIN MAJOR-HOMOLOGY-REGION PEPTIDE ANALOGS BY NMR JRNL TITL 4 SPECTROSCOPY. JRNL REF EUR.J.BIOCHEM. V. 257 69 1998 JRNL REFN ISSN 0014-2956 JRNL PMID 9799104 JRNL DOI 10.1046/J.1432-1327.1998.2570069.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1BMX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171923. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 90/10 H20/D20 50% TFE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : AMX400 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BIOSYM FELIX FELIX, FELIX ASSIGN REMARK 210 ASSIGN, DGII, DISCOVER REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLOATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STUCTURE WAS DETERMINED WITH 2D-1H-NMR AND A SYNTHETIC REMARK 210 PEPTIDE (5-7 MILLIMOLAR) 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: CLOSE CONTACTS 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 ARG A 20 HG1 THR A 24 1.55 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 1 GLU A 12 CD GLU A 12 OE2 0.111 REMARK 500 1 GLU A 28 CD GLU A 28 OE2 0.109 REMARK 500 1 SER A 31 C SER A 31 OXT 0.141 REMARK 500 2 GLU A 12 CD GLU A 12 OE2 0.109 REMARK 500 2 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 2 SER A 31 C SER A 31 OXT 0.142 REMARK 500 3 GLU A 12 CD GLU A 12 OE2 0.110 REMARK 500 3 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 3 SER A 31 C SER A 31 OXT 0.136 REMARK 500 4 GLU A 12 CD GLU A 12 OE2 0.109 REMARK 500 4 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 4 SER A 31 C SER A 31 OXT 0.135 REMARK 500 5 GLU A 12 CD GLU A 12 OE2 0.111 REMARK 500 5 GLU A 28 CD GLU A 28 OE2 0.109 REMARK 500 5 SER A 31 C SER A 31 OXT 0.136 REMARK 500 6 GLU A 12 CD GLU A 12 OE2 0.113 REMARK 500 6 GLU A 28 CD GLU A 28 OE2 0.111 REMARK 500 6 SER A 31 C SER A 31 OXT 0.144 REMARK 500 7 GLU A 12 CD GLU A 12 OE2 0.110 REMARK 500 7 GLU A 28 CD GLU A 28 OE2 0.108 REMARK 500 7 SER A 31 C SER A 31 OXT 0.140 REMARK 500 8 GLU A 12 CD GLU A 12 OE2 0.111 REMARK 500 8 GLU A 28 CD GLU A 28 OE2 0.109 REMARK 500 8 SER A 31 C SER A 31 OXT 0.133 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 1 ASP A 5 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ASP A 16 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 ASP A 16 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 ASP A 19 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 ASP A 19 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 ARG A 20 N - CA - CB ANGL. DEV. = -12.7 DEGREES REMARK 500 1 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ASP A 16 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 ASP A 19 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 ASP A 19 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 ARG A 20 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 2 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ASP A 5 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 3 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ASP A 16 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 3 ASP A 16 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 3 ASP A 19 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 3 ARG A 20 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 3 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 4 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ASP A 16 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 4 ASP A 19 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 4 ASP A 19 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 4 ARG A 20 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 4 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ASP A 5 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 ASP A 5 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 5 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ASP A 16 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 5 ASP A 16 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 5 ASP A 19 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 ASP A 19 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 5 ARG A 20 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 5 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 80 ANGLE DEVIATIONS. 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 1 SER A 2 -79.14 -148.84 REMARK 500 1 ASP A 5 -65.63 -139.43 REMARK 500 1 GLN A 8 87.11 63.53 REMARK 500 1 LYS A 11 -71.89 -134.89 REMARK 500 1 ARG A 26 31.52 -83.55 REMARK 500 1 ALA A 30 115.43 -168.64 REMARK 500 2 SER A 2 -67.27 -157.62 REMARK 500 2 LEU A 4 41.24 -95.80 REMARK 500 2 ASP A 5 -67.21 -153.85 REMARK 500 2 ARG A 7 -31.67 -170.13 REMARK 500 2 GLU A 12 -55.46 104.30 REMARK 500 2 ARG A 26 36.20 -92.57 REMARK 500 3 ASP A 5 -66.16 -100.35 REMARK 500 3 LYS A 11 -44.14 -173.67 REMARK 500 3 PHE A 14 25.96 -78.49 REMARK 500 3 ALA A 30 84.16 72.70 REMARK 500 4 SER A 2 -65.84 -103.39 REMARK 500 4 ASP A 5 -40.42 -154.48 REMARK 500 4 LYS A 11 -72.09 -130.26 REMARK 500 4 ARG A 26 33.98 -83.20 REMARK 500 4 ALA A 27 -33.74 -132.54 REMARK 500 5 ASP A 5 -75.42 -131.09 REMARK 500 5 ARG A 7 39.34 -92.33 REMARK 500 5 LYS A 11 -61.99 -138.26 REMARK 500 5 PRO A 13 -155.91 -86.87 REMARK 500 5 PHE A 14 57.01 -154.59 REMARK 500 5 ALA A 30 75.76 55.95 REMARK 500 6 SER A 2 -77.50 -117.14 REMARK 500 6 GLN A 8 73.84 64.41 REMARK 500 6 LYS A 11 -40.68 64.24 REMARK 500 6 PHE A 14 1.77 46.38 REMARK 500 7 LEU A 4 39.55 -84.92 REMARK 500 7 ARG A 7 43.60 -104.34 REMARK 500 7 LYS A 11 -65.89 -137.92 REMARK 500 7 ALA A 30 -63.78 66.65 REMARK 500 8 SER A 2 -104.49 -166.05 REMARK 500 8 ILE A 3 36.80 34.98 REMARK 500 8 LEU A 4 43.24 38.91 REMARK 500 8 ASP A 5 -58.21 -162.72 REMARK 500 8 GLN A 8 80.57 59.42 REMARK 500 8 LYS A 11 -54.54 -134.29 REMARK 500 8 ALA A 30 -67.84 65.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 15 ASP A 16 1 145.94 REMARK 500 ARG A 26 ALA A 27 1 138.43 REMARK 500 ARG A 26 ALA A 27 2 133.16 REMARK 500 PHE A 14 ARG A 15 3 148.10 REMARK 500 ARG A 26 ALA A 27 3 143.29 REMARK 500 ARG A 15 ASP A 16 4 147.85 REMARK 500 ARG A 15 ASP A 16 5 141.44 REMARK 500 ARG A 15 ASP A 16 6 144.45 REMARK 500 ARG A 15 ASP A 16 7 141.29 REMARK 500 ARG A 26 ALA A 27 7 140.14 REMARK 500 ARG A 26 ALA A 27 8 137.44 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 1 TYR A 17 0.08 SIDE CHAIN REMARK 500 2 TYR A 17 0.08 SIDE CHAIN REMARK 500 3 TYR A 17 0.08 SIDE CHAIN REMARK 500 4 TYR A 17 0.09 SIDE CHAIN REMARK 500 6 TYR A 17 0.10 SIDE CHAIN REMARK 500 7 TYR A 17 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BMX A 1 31 UNP Q76258 Q76258_9HIV1 66 96 SEQADV 1BMX SER A 2 UNP Q76258 GLY 67 CONFLICT SEQRES 1 A 31 CYS SER ILE LEU ASP ILE ARG GLN GLY PRO LYS GLU PRO SEQRES 2 A 31 PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS THR LEU ARG SEQRES 3 A 31 ALA GLU GLN ALA SER HELIX 1 1 PHE A 14 ARG A 26 1 13 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