HEADER VIRAL PROTEIN 08-AUG-02 1MEQ TITLE HIV GP120 C5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTERIOR MEMBRANE GLYCOPROTEIN (GP120); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES (484-506); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SOURCE 4 SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HUMAN SOURCE 5 IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1). KEYWDS HIV, AIDS, GP120, GP41, VIRAL PROTEIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.CAFFREY,A.JACOBS,L.GUILHAUDIS REVDAT 2 24-FEB-09 1MEQ 1 VERSN REVDAT 1 11-DEC-02 1MEQ 0 JRNL AUTH L.GUILHAUDIS,A.JACOBS,M.CAFFREY JRNL TITL SOLUTION STRUCTURE OF THE HIV GP120 C5 DOMAIN JRNL REF EUR.J.BIOCHEM. V. 269 4860 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 12354117 JRNL DOI 10.1046/J.1432-1033.2002.03187.X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, A., ADAMS, P., CLORE, G., DELANO, W., REMARK 3 GROS, P., GROSSE-KUNSTLEVE, R., JIANG, J.-S., REMARK 3 KUSZEWSKI, J., NILGES, M., PANNU, N., READ, R., REMARK 3 RICE, L., SIMONSON, T. & WARREN, G. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 190 DISTANCE RESTRAINTS, 47 DIHEDRAL REMARK 3 RESTRAINTS REMARK 4 REMARK 4 1MEQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016858. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 70 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM HIV GP120 C5 AT NATURAL REMARK 210 ABUNDANCE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 ARG A 15 CG ARG A 15 CD -0.162 REMARK 500 LYS A 22 CA LYS A 22 CB -0.158 REMARK 500 ARG A 23 CB ARG A 23 CG -0.238 REMARK 500 ARG A 23 CD ARG A 23 NE -0.145 REMARK 500 ARG A 23 CZ ARG A 23 NH2 0.119 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 ARG A 15 CD - NE - CZ ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG A 15 NE - CZ - NH1 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 16 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 20 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 23 CG - CD - NE ANGL. DEV. = -20.8 DEGREES REMARK 500 ARG A 23 CD - NE - CZ ANGL. DEV. = -19.2 DEGREES REMARK 500 ARG A 23 NE - CZ - NH1 ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES 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 LEU A 6 -3.89 -51.60 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 ARG A 16 0.08 SIDE_CHAIN REMARK 500 ARG A 20 0.08 SIDE_CHAIN REMARK 500 ARG A 23 0.36 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1MEQ A 1 23 UNP P19549 ENV_HV1S3 484 506 SEQRES 1 A 23 VAL LYS ILE GLU PRO LEU GLY VAL ALA PRO THR LYS ALA SEQRES 2 A 23 LYS ARG ARG VAL VAL GLN ARG GLU LYS ARG HELIX 1 1 PRO A 10 LYS A 22 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 MASTER 136 0 0 1 0 0 0 6 0 0 0 2 END