10 20 30 40 50 60 70 80 5HIR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER COAGULATION INHIBITOR 09-JAN-90 5HIR
TITLE SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 TITLE 2 (RIGHT ARROW) GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND TITLE 3 HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING TITLE 4 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 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 JRNL TITL 3 AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED JRNL TITL 4 ANNEALING STUDY. JRNL REF BIOCHEMISTRY V. 28 2601 1989 JRNL REFN ISSN 0006-2960 JRNL PMID 2567183 JRNL DOI 10.1021/BI00432A038
REMARK 1
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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 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