Header list of 5hir.pdb file
Complete list - 29 201 Bytes
HEADER COAGULATION INHIBITOR 09-JAN-90 5HIR
TITLE SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 (RIGHT ARROW)
TITLE 2 GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE
TITLE 3 GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HIRUDIN VARIANT-1;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS;
SOURCE 3 ORGANISM_COMMON: MEDICINAL LEECH;
SOURCE 4 ORGANISM_TAXID: 6421
KEYWDS COAGULATION INHIBITOR
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,A.M.GRONENBORN
REVDAT 4 29-NOV-17 5HIR 1 REMARK HELIX
REVDAT 3 24-FEB-09 5HIR 1 VERSN
REVDAT 2 01-APR-03 5HIR 1 JRNL
REVDAT 1 15-JAN-90 5HIR 0
JRNL AUTH P.J.FOLKERS,G.M.CLORE,P.C.DRISCOLL,J.DODT,S.KOHLER,
JRNL AUTH 2 A.M.GRONENBORN
JRNL TITL SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE
JRNL TITL 2 LYS-47----GLU MUTANT: A NUCLEAR MAGNETIC RESONANCE AND
JRNL TITL 3 HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
JRNL TITL 4 STUDY.
JRNL REF BIOCHEMISTRY V. 28 2601 1989
JRNL REFN ISSN 0006-2960
JRNL PMID 2567183
JRNL DOI 10.1021/BI00432A038
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE METHOD USED TO DETERMINE AND REFINE THE
REMARK 3 STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE
REMARK 3 GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD
REMARK 3 (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229,
REMARK 3 317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER,
REMARK 3 YALE UNIVERSITY, CT 06511).
REMARK 3
REMARK 3 STRUCTURAL STATISTICS
REMARK 3
REMARK 3 RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)*
REMARK 3
REMARK 3 RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS)
REMARK 3
REMARK 3 ALL 701 0.075
REMARK 3 INTERRESIDUE
REMARK 3 SHORT RANGE 242 0.094
REMARK 3 INTERRESIDUE
REMARK 3 LONG RANGE 208 0.057
REMARK 3 INTRARESIDUE 235 0.067
REMARK 3 HBOND *(2)* 16 0.052
REMARK 3
REMARK 3 POTENTIAL ENERGY TERMS
REMARK 3
REMARK 3 TYPE ENERGY (KCAL/MOL)
REMARK 3
REMARK 3 F(NOE) *(3)* 196
REMARK 3 F(TOR) *(4)* 14
REMARK 3 F(REPEL) *(5)* 45
REMARK 3
REMARK 3 LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
REMARK 3 USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
REMARK 3 -73 KCAL/MOL.
REMARK 3
REMARK 3 DEVIATIONS FROM IDEALIZED GEOMETRY *(6)*
REMARK 3
REMARK 3 TYPE TOTAL NUMBER RMS DEVIATION
REMARK 3
REMARK 3 BONDS 676 0.012 (ANGSTROMS)
REMARK 3 ANGLES 1223 1.814 (DEGREES)
REMARK 3 IMPROPERS 131 0.597 (DEGREES)
REMARK 3
REMARK 3 NOTES.
REMARK 3 *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS
REMARK 3 ARE CALCULATED WITH RESPECT TO THE UPPER AND
REMARK 3 LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF
REMARK 3 THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN
REMARK 3 0.5 ANGSTROMS.
REMARK 3 *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO
REMARK 3 RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND
REMARK 3 R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS
REMARK 3 ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII
REMARK 3 OF THE RELEVANT ATOMS.
REMARK 3 *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL
REMARK 3 F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF
REMARK 3 50 KCAL/MOL/ANGSTROM**2.
REMARK 3 *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE
REMARK 3 CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A
REMARK 3 SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO
REMARK 3 RESTRICT THE RANGES OF 33 PHI ,24 PSI AND 25 CHI1
REMARK 3 TORSION ANGLES.
REMARK 3 *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM
REMARK 3 F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF
REMARK 3 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE
REMARK 3 VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD
REMARK 3 VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY
REMARK 3 FUNCTION.
REMARK 3 *(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY
REMARK 3 AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE
REMARK 3 PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION
REMARK 3 OF PROLINES) IN THE TRANS CONFORMATION. IN THE
REMARK 3 DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE
REMARK 3 RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED
REMARK 3 IN THE BOND AND ANGLE TERMS.
REMARK 3
REMARK 3 A TOTAL OF 32 STRUCTURES CONSISTENT WITH THE NMR DATA
REMARK 3 WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES
REMARK 3 OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL
REMARK 3 STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO
REMARK 3 FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THE
REMARK 3 32 STRUCTURES ARE GIVEN IN THE PROTEIN DATA BANK ENTRY
REMARK 3 *2HIR*.
REMARK 3
REMARK 3 THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE
REMARK 3 ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT
REMARK 3 THE MEAN COORDINATE POSITIONS.
REMARK 3
REMARK 3 ONLY RESIDUES 1-49 ARE WELL DEFINED. RESIDUES 50-65 FORM
REMARK 3 A DISORDERED C-TERMINAL TAIL.
REMARK 4
REMARK 4 5HIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000179723.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
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 : NULL
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 SER A 50
REMARK 465 HIS A 51
REMARK 465 ASN A 52
REMARK 465 ASP A 53
REMARK 465 GLY A 54
REMARK 465 ASP A 55
REMARK 465 PHE A 56
REMARK 465 GLU A 57
REMARK 465 GLU A 58
REMARK 465 ILE A 59
REMARK 465 PRO A 60
REMARK 465 GLU A 61
REMARK 465 GLU A 62
REMARK 465 TYR A 63
REMARK 465 LEU A 64
REMARK 465 GLN A 65
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 TYR A 3 -122.65 -84.60
REMARK 500 CYS A 6 167.43 -48.55
REMARK 500 THR A 7 2.79 -156.13
REMARK 500 ASN A 12 -60.15 -148.98
REMARK 500 CYS A 16 -80.17 -79.71
REMARK 500 CYS A 22 -149.44 -77.85
REMARK 500 ASN A 26 -158.73 -103.20
REMARK 500 LEU A 30 -168.42 -76.35
REMARK 500 SER A 32 54.23 -161.55
REMARK 500 ASP A 33 72.15 56.60
REMARK 500 GLN A 38 106.50 -161.59
REMARK 500 LYS A 47 107.59 -44.20
REMARK 500 PRO A 48 171.53 -59.46
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2HIR RELATED DB: PDB
DBREF 5HIR A 1 65 UNP P01050 ITH1_HIRME 1 65
SEQRES 1 A 65 VAL VAL TYR THR ASP CYS THR GLU SER GLY GLN ASN LEU
SEQRES 2 A 65 CYS LEU CYS GLU GLY SER ASN VAL CYS GLY GLN GLY ASN
SEQRES 3 A 65 LYS CYS ILE LEU GLY SER ASP GLY GLU LYS ASN GLN CYS
SEQRES 4 A 65 VAL THR GLY GLU GLY THR PRO LYS PRO GLN SER HIS ASN
SEQRES 5 A 65 ASP GLY ASP PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN
SHEET 1 A 3 SER A 9 GLN A 11 0
SHEET 2 A 3 LYS A 27 GLY A 31 -1
SHEET 3 A 3 LYS A 36 VAL A 40 -1
SHEET 1 B 2 CYS A 14 CYS A 16 0
SHEET 2 B 2 VAL A 21 CYS A 22 -1
SSBOND 1 CYS A 6 CYS A 14 1555 1555 2.02
SSBOND 2 CYS A 16 CYS A 28 1555 1555 2.02
SSBOND 3 CYS A 22 CYS A 39 1555 1555 2.02
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
Complete list - 29 201 Bytes