10 20 30 40 50 60 70 80 1BM4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 28-JUL-98 1BM4
TITLE MOMLV CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MOLONEY MURINE LEUKEMIA VIRUS CAPSID); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MAJOR HOMOLOGY REGION PEPTIDE, N-TERMINAL CYS; COMPND 5 SYNONYM: MOMLV CA MHR PEPTIDE ANALOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED FROM SOURCE 4 MOLONEY MURINE LEUKEMIA VIRUS (MOMLV).
KEYWDS MOLONEY MURINE LEUKEMIA VIRUS CAPSID PROTEIN, MOMLV, MU-MLV, KEYWDS 2 CAPSID, MHR, MAJOR HOMOLOGY REGION, VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR C.B.CLISH,D.H.PEYTON,E.BARKLIS
REVDAT 4 24-FEB-09 1BM4 1 VERSN REVDAT 3 01-APR-03 1BM4 1 JRNL REVDAT 2 29-DEC-99 1BM4 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 05-AUG-98 1BM4 0
JRNL AUTH C.B.CLISH,D.H.PEYTON,E.BARKLIS JRNL TITL SOLUTION STRUCTURES OF HUMAN IMMUNODEFICIENCY JRNL TITL 2 VIRUS TYPE 1 (HIV-1) AND MOLONEY MURINE LEUKEMIA JRNL TITL 3 VIRUS (MOMLV) CAPSID PROTEIN MAJOR-HOMOLOGY-REGION JRNL TITL 4 PEPTIDE ANALOGS BY NMR 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 1
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 REMARK 3 THE JRNL CITATION ABOVE
REMARK 4 REMARK 4 1BM4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB008214.
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 : NULL 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 REMARK 210 ASSIGN ASSIGN, DGII, DISCOVER REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH 2D-1H-NMR AND A REMARK 210 SYNTHETIC 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 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 13 CD GLU A 13 OE2 0.110 REMARK 500 1 GLU A 20 CD GLU A 20 OE2 0.110 REMARK 500 1 GLU A 24 CD GLU A 24 OE2 0.109 REMARK 500 1 TYR A 32 C TYR A 32 OXT 0.135 REMARK 500 2 GLU A 13 CD GLU A 13 OE2 0.109 REMARK 500 2 GLU A 20 CD GLU A 20 OE2 0.108 REMARK 500 2 GLU A 24 CD GLU A 24 OE2 0.110 REMARK 500 2 TYR A 32 C TYR A 32 OXT 0.136 REMARK 500 3 GLU A 13 CD GLU A 13 OE2 0.109 REMARK 500 3 GLU A 20 CD GLU A 20 OE2 0.111 REMARK 500 3 GLU A 24 CD GLU A 24 OE2 0.115 REMARK 500 3 TYR A 32 C TYR A 32 OXT 0.135 REMARK 500 4 GLU A 13 CD GLU A 13 OE2 0.110 REMARK 500 4 GLU A 20 CD GLU A 20 OE2 0.109 REMARK 500 4 GLU A 24 CD GLU A 24 OE2 0.110 REMARK 500 4 TYR A 32 C TYR A 32 OXT 0.145 REMARK 500 5 GLU A 13 CD GLU A 13 OE2 0.109 REMARK 500 5 GLU A 20 CD GLU A 20 OE2 0.110 REMARK 500 5 GLU A 24 CD GLU A 24 OE2 0.109 REMARK 500 5 TYR A 32 C TYR A 32 OXT 0.136 REMARK 500 6 GLU A 13 CD GLU A 13 OE2 0.109 REMARK 500 6 GLU A 20 CD GLU A 20 OE2 0.114 REMARK 500 6 GLU A 24 CD GLU A 24 OE2 0.115 REMARK 500 6 TYR A 32 C TYR A 32 OXT 0.143 REMARK 500 7 GLU A 13 CD GLU A 13 OE2 0.110 REMARK 500 7 GLU A 20 CD GLU A 20 OE2 0.110 REMARK 500 7 GLU A 24 CD GLU A 24 OE2 0.108 REMARK 500 7 TYR A 32 C TYR A 32 OXT 0.136 REMARK 500 8 GLU A 13 CD GLU A 13 OE2 0.111 REMARK 500 8 GLU A 20 CD GLU A 20 OE2 0.111 REMARK 500 8 GLU A 24 CD GLU A 24 OE2 0.111 REMARK 500 8 TYR A 32 C TYR A 32 OXT 0.142 REMARK 500 9 GLU A 13 CD GLU A 13 OE2 0.109 REMARK 500 9 GLU A 20 CD GLU A 20 OE2 0.113 REMARK 500 9 GLU A 24 CD GLU A 24 OE2 0.110 REMARK 500 9 TYR A 32 C TYR A 32 OXT 0.134 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 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 SER A 16 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 TYR A 26 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 5 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 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 1 VAL A 4 79.72 -105.05 REMARK 500 1 GLN A 9 93.72 73.79 REMARK 500 1 PRO A 11 94.45 -51.70 REMARK 500 1 GLU A 13 36.61 34.32 REMARK 500 1 THR A 30 113.39 -169.60 REMARK 500 2 VAL A 4 49.79 -92.20 REMARK 500 2 LYS A 5 73.00 -158.76 REMARK 500 2 ASN A 12 79.15 61.77 REMARK 500 2 SER A 16 84.27 -170.68 REMARK 500 2 ALA A 17 -37.88 -148.53 REMARK 500 2 ARG A 27 54.00 -105.10 REMARK 500 2 ARG A 28 -37.50 -169.41 REMARK 500 3 LYS A 3 -79.05 66.98 REMARK 500 3 LYS A 5 81.70 179.57 REMARK 500 3 THR A 8 -73.54 -143.30 REMARK 500 3 PRO A 15 -156.16 -92.20 REMARK 500 3 SER A 16 44.60 16.99 REMARK 500 3 PHE A 18 -47.57 68.58 REMARK 500 4 LYS A 3 70.05 53.38 REMARK 500 4 VAL A 4 90.38 46.40 REMARK 500 4 LYS A 5 82.50 -151.23 REMARK 500 4 PRO A 11 45.86 -78.04 REMARK 500 4 SER A 16 80.59 -164.19 REMARK 500 4 ALA A 17 -42.47 -147.42 REMARK 500 5 LYS A 3 107.49 91.91 REMARK 500 5 VAL A 4 68.07 -104.03 REMARK 500 5 GLU A 13 -15.30 65.19 REMARK 500 5 ARG A 28 -55.76 -166.66 REMARK 500 6 LYS A 5 77.60 -165.86 REMARK 500 6 GLN A 9 66.52 -155.32 REMARK 500 6 PRO A 11 105.26 -56.56 REMARK 500 7 THR A 8 -62.63 -155.75 REMARK 500 7 PRO A 11 84.50 -63.06 REMARK 500 7 SER A 14 -69.20 -121.82 REMARK 500 7 SER A 16 -110.21 66.64 REMARK 500 7 ALA A 17 -60.19 62.13 REMARK 500 7 ARG A 28 -55.34 -158.27 REMARK 500 8 LYS A 3 104.34 -163.16 REMARK 500 8 VAL A 4 70.72 44.42 REMARK 500 8 LYS A 5 72.37 -160.42 REMARK 500 8 GLN A 9 75.87 50.54 REMARK 500 8 SER A 16 -89.14 66.30 REMARK 500 8 ALA A 17 -72.55 58.54 REMARK 500 9 ALA A 2 37.50 -89.68 REMARK 500 9 LYS A 3 -59.62 -162.94 REMARK 500 9 LYS A 5 44.29 -157.05 REMARK 500 9 THR A 8 -80.42 -105.42 REMARK 500 9 GLN A 9 82.18 -150.42 REMARK 500 9 ALA A 17 -48.88 65.01 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 GLN A 9 GLY A 10 3 -147.81 REMARK 500 LYS A 5 GLY A 6 5 -141.38 REMARK 500 GLN A 9 GLY A 10 5 -132.18 REMARK 500 GLN A 9 GLY A 10 6 -137.65 REMARK 500 LYS A 5 GLY A 6 7 -145.09 REMARK 500 GLN A 9 GLY A 10 7 -135.62 REMARK 500 GLU A 13 SER A 14 7 144.36 REMARK 500 GLN A 9 GLY A 10 8 -36.05 REMARK 500 VAL A 4 LYS A 5 9 149.45 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 4 TYR A 29 0.08 SIDE_CHAIN REMARK 500 6 ARG A 28 0.09 SIDE_CHAIN REMARK 500 6 TYR A 29 0.06 SIDE_CHAIN REMARK 500 8 TYR A 29 0.10 SIDE_CHAIN REMARK 500 9 TYR A 29 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1BM4 A 1 32 UNP Q9WJP4 Q9WJP4_MLVMO 352 383
SEQADV 1BM4 CYS A 1 UNP Q9WJP4 LEU 352 MUTATION
SEQRES 1 A 32 CYS ALA LYS VAL LYS GLY ILE THR GLN GLY PRO ASN GLU SEQRES 2 A 32 SER PRO SER ALA PHE LEU GLU ARG LEU LYS GLU ALA TYR SEQRES 3 A 32 ARG ARG TYR THR PRO TYR
HELIX 1 1 PRO A 11 GLU A 13 5 3 HELIX 2 2 SER A 16 ARG A 28 1 13 HELIX 3 3 GLU A 13 SER A 16 1 4 HELIX 4 4 PHE A 18 TYR A 26 1 9 HELIX 5 5 LEU A 19 TYR A 29 1 11 HELIX 6 9 PHE A 18 TYR A 29 1 12 HELIX 7 7 SER A 16 TYR A 26 1 11 HELIX 8 8 ASN A 12 TYR A 29 1 18 HELIX 9 12 PHE A 18 ARG A 28 1 11 HELIX 10 11 ASN A 12 PRO A 15 1 4
CISPEP 1 GLY A 6 ILE A 7 1 -3.92 CISPEP 2 GLN A 9 GLY A 10 1 -24.63 CISPEP 3 SER A 14 PRO A 15 3 -6.47 CISPEP 4 GLN A 9 GLY A 10 4 -29.97 CISPEP 5 ALA A 2 LYS A 3 7 -22.83 CISPEP 6 GLN A 9 GLY A 10 9 -24.21
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