10 20 30 40 50 60 70 80 1DWD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYROLASE INHIBITOR 19-AUG-92 1DWD
TITLE CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TITLE 2 TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-THROMBIN (SMALL SUBUNIT); COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ALPHA-THROMBIN (LARGE SUBUNIT); COMPND 8 CHAIN: H; COMPND 9 EC: 3.4.21.5; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIRUDIN IIIA; COMPND 13 CHAIN: I; COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 ORGAN: PLASMA; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 13 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 14 ORGANISM_TAXID: 6421
KEYWDS SERINE PROTEINASE, HYDROLASE-HYROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR D.W.BANNER,P.HADVARY
REVDAT 5 13-JUL-11 1DWD 1 VERSN REVDAT 4 24-FEB-09 1DWD 1 VERSN REVDAT 3 01-APR-03 1DWD 1 JRNL REVDAT 2 15-MAY-95 1DWD 1 HET REVDAT 1 31-JAN-94 1DWD 0
JRNL AUTH D.W.BANNER,P.HADVARY JRNL TITL CRYSTALLOGRAPHIC ANALYSIS AT 3.0-A RESOLUTION OF THE BINDING JRNL TITL 2 TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS. JRNL REF J.BIOL.CHEM. V. 266 20085 1991 JRNL REFN ISSN 0021-9258 JRNL PMID 1939071
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.BODE,D.TURK,J.STURZEBECHER REMARK 1 TITL GEOMETRY OF BINDING OF THE BENZAMIDINE- AND ARGININE-BASED REMARK 1 TITL 2 INHIBITORS N REMARK 1 TITL 3 ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P- REMARK 1 TITL 4 AMIDINOPHENYLALANYL-PIPE RIDINE (NAPAP) AND REMARK 1 TITL 5 (2R,4R)-4-METHYL-1-[N ALPHA-(3-METHYL-1,2,3,4-TETRAHYDRO-8- REMARK 1 TITL 6 QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC ACID REMARK 1 TITL 7 (MQPA) TO HUMAN ALPHA-THROMBIN. X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 8 DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF REMARK 1 TITL 9 NAPAP-THROMBIN AND MQPA-THROMBIN. REMARK 1 REF EUR.J.BIOCHEM. V. 193 175 1990 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 2226434 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.BODE,I.MAYR,U.BAUMANN,R.HUBER,S.R.STONE,J.HOFSTEENGE REMARK 1 TITL THE REFINED 1.9 A CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: REMARK 1 TITL 2 INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND REMARK 1 TITL 3 SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT. REMARK 1 REF EMBO J. V. 8 3467 1989 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 2583108 REMARK 1 REFERENCE 3 REMARK 1 AUTH W.BODE,D.TURK,A.KARSHIKOV REMARK 1 TITL THE REFINED 1.9-A X-RAY CRYSTAL STRUCTURE OF D-PHE-PRO-ARG REMARK 1 TITL 2 CHLOROMETHYLKETONE-INHIBITED HUMAN ALPHA-THROMBIN: STRUCTURE REMARK 1 TITL 3 ANALYSIS, OVERALL STRUCTURE, ELECTROSTATIC PROPERTIES, REMARK 1 TITL 4 DETAILED ACTIVE-SITE GEOMETRY, AND STRUCTURE-FUNCTION REMARK 1 TITL 5 RELATIONSHIPS. REMARK 1 REF PROTEIN SCI. V. 1 426 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 1304349 REMARK 1 REFERENCE 4 REMARK 1 AUTH T.J.RYDEL,K.G.RAVICHANDRAN,A.TULINSKY,W.BODE,R.HUBER, REMARK 1 AUTH 2 C.ROITSCH,J.W.FENTON REMARK 1 TITL THE STRUCTURE OF A COMPLEX OF RECOMBINANT HIRUDIN AND HUMAN REMARK 1 TITL 2 ALPHA-THROMBIN. REMARK 1 REF SCIENCE V. 249 277 1990 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 2374926 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.T.STUBBS,H.OSCHKINAT,I.MAYR,R.HUBER,H.ANGLIKER,S.R.STONE, REMARK 1 AUTH 2 W.BODE REMARK 1 TITL THE INTERACTION OF THROMBIN WITH FIBRINOGEN. A STRUCTURAL REMARK 1 TITL 2 BASIS FOR ITS SPECIFICITY. REMARK 1 REF EUR.J.BIOCHEM. V. 206 187 1992 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 1587268 REMARK 1 REFERENCE 6 REMARK 1 AUTH M.G.GRUTTER,J.P.PRIESTLE,J.RAHUEL,H.GROSSENBACHER,W.BODE, REMARK 1 AUTH 2 J.HOFSTEENGE,S.R.STONE REMARK 1 TITL CRYSTAL STRUCTURE OF THE THROMBIN-HIRUDIN COMPLEX: A NOVEL REMARK 1 TITL 2 MODE OF SERINE PROTEASE INHIBITION. REMARK 1 REF EMBO J. V. 9 2361 1990 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 2369893
REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2358 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.015 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.980 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PROLINES ARE TOO FLAT AS A BAD DICTIONARY WAS USED. REMARK 3 REMARK 3 ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS REMARK 3 WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR.
REMARK 4 REMARK 4 1DWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.40000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 99.37500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.40000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 99.37500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.12500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.25000 REMARK 290 REMARK 290 REMARK: NULL
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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 400 REMARK 400 COMPOUND REMARK 400 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN REMARK 400 INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN REMARK 400 INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN REMARK 400 INDICATOR *I* IS USED FOR A C-TERMINAL HIRUDIN PEPTIDE REMARK 400 ((DES-AMINO ASP55)HIRUDIN(55-65)). THE RESIDUES OF REMARK 400 CHAIN I ARE NUMBERED FROM 1 - 11. IT BINDS IN THE REMARK 400 ANION-BINDING EXOSITE.
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR L 1H REMARK 465 PHE L 1G REMARK 465 GLY L 1F REMARK 465 SER L 1E REMARK 465 GLY L 1D REMARK 465 GLY L 14M REMARK 465 ARG L 14N REMARK 465 GLU H 247
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 470 ARG H 77A CG CD NE CZ NH1 NH2 REMARK 470 ASN H 78 CG OD1 REMARK 470 LYS H 81 CG CD CE NZ REMARK 470 ARG H 93 CG CD NE CZ NH1 NH2 REMARK 470 ARG H 97 CG CD NE CZ NH1 NH2 REMARK 470 GLU H 127 CG CD OE1 OE2 REMARK 470 LYS H 149E CG CD CE NZ REMARK 470 LYS H 169 CG CD CE NZ REMARK 470 ARG H 173 CG CD NE CZ NH1 NH2 REMARK 470 GLY H 246 CA C O REMARK 470 ASP I 1 N REMARK 470 GLU I 8 CG CD OE1 OE2 REMARK 470 GLN I 11 CA C O CB CG CD OE1 REMARK 470 GLN I 11 NE2
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 GLU L 14E CD GLU L 14E OE1 0.089 REMARK 500 GLU H 18 CD GLU H 18 OE2 0.083 REMARK 500 GLU H 39 CD GLU H 39 OE2 0.076 REMARK 500 GLU H 61 CD GLU H 61 OE1 0.068 REMARK 500 GLU H 86 CD GLU H 86 OE2 0.078 REMARK 500 GLU H 97A CD GLU H 97A OE1 0.076 REMARK 500 GLU H 186B CD GLU H 186B OE2 0.075 REMARK 500 GLU H 192 CD GLU H 192 OE2 0.084 REMARK 500 GLU I 4 CD GLU I 4 OE2 0.095 REMARK 500 GLU I 7 CD GLU I 7 OE2 0.072 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 ASP L 14L CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP H 60E CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP H 60E CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ASP H 100 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP H 102 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP H 116 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP H 125 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP H 170 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP H 170 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP H 178 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG H 187 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP H 189 CB - CG - OD1 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP H 189 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP H 243 CB - CG - OD2 ANGL. DEV. = -5.6 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 PHE L 7 -85.65 -125.25 REMARK 500 SER L 11 19.73 58.70 REMARK 500 SER H 48 169.59 174.77 REMARK 500 ASP H 49 -29.10 -37.02 REMARK 500 HIS H 57 -4.63 -50.80 REMARK 500 TYR H 60A 79.30 -156.07 REMARK 500 PRO H 60C -4.69 -41.49 REMARK 500 ASN H 60G 79.10 -160.70 REMARK 500 HIS H 71 -58.01 -122.57 REMARK 500 SER H 115 -159.03 -154.96 REMARK 500 ASN H 149B -3.17 58.50 REMARK 500 VAL H 149C 73.77 -107.47 REMARK 500 LYS H 149E 107.67 -163.97 REMARK 500 SER H 214 -74.12 -109.31 REMARK 500 GLN H 244 4.96 -65.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP L 1A 19.2 L L OUTSIDE RANGE REMARK 500 SER L 11 24.0 L L OUTSIDE RANGE REMARK 500 LYS L 14A 24.8 L L OUTSIDE RANGE REMARK 500 ASP L 14L 24.1 L L OUTSIDE RANGE REMARK 500 GLU H 186B 23.9 L L OUTSIDE RANGE REMARK 500 GLU I 4 24.9 L L OUTSIDE RANGE REMARK 500 GLU I 7 24.1 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 600 REMARK 600 HETEROGEN REMARK 600 NAPAP IS N==ALPHA==-(2-NAPHTHYL-SULFONYL-GLYCYL)-(DL)- REMARK 600 PARA-AMIDINOPHENYLALANYL-PIPERIDINE (STUERZEBECHER ET AL., REMARK 600 THROMB. RES. VOL 29 PP 635-642 (1983)). THE AUTHORS SHOW REMARK 600 HERE THAT THE D-ISOMER BINDS TO THROMBIN.
REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4- REMARK 630 CARBAMIMIDOYL-D-PHENYLALANYL]PIPERIDINE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 MID H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NAS GLY APH PIP REMARK 630 DETAILS: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MID H 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIIA
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DWB RELATED DB: PDB REMARK 900 RELATED ID: 1DWC RELATED DB: PDB REMARK 900 RELATED ID: 1DWE RELATED DB: PDB
DBREF 1DWD L 1H 14N UNP P00734 THRB_HUMAN 328 363 DBREF 1DWD H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1DWD I 1 11 UNP P28508 ITHH_HIRME 55 65
SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN
HET MID H 1 37
HETNAM MID 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4-CARBAMIMIDOYL-D- HETNAM 2 MID PHENYLALANYL]PIPERIDINE
HETSYN MID NAPAP
FORMUL 4 MID C27 H31 N5 O4 S FORMUL 5 HOH *50(H2 O)
HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B SER L 14I 1 8 HELIX 3 3 ALA H 55 CYS H 58 5 4 HELIX 4 4 PRO H 60B ASP H 60E 5 4 HELIX 5 5 ASP H 125 LEU H 130 1 9 HELIX 6 6 GLU H 164 ASP H 170 1 7 HELIX 7 7 LYS H 185 GLY H 186C 5 5 HELIX 8 8 LEU H 234 ASP H 243 1 10 HELIX 9 9 PRO I 6 LEU I 10 5 5
SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 N VAL H 157 O SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 A 7 TRP H 207 TRP H 215 -1 N TYR H 208 O MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 N PHE H 227 O TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 B 7 GLN H 30 ARG H 35 0 SHEET 2 B 7 GLU H 39 SER H 48 -1 O GLU H 39 N ARG H 35 SHEET 3 B 7 TRP H 51 THR H 54 -1 O TRP H 51 N ILE H 47 SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 B 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 B 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85 SHEET 7 B 7 GLN H 30 ARG H 35 -1 N MET H 32 O ARG H 67
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.02 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 1.95
CISPEP 1 SER H 36A PRO H 37 0 -1.03
SITE 1 ACT 3 HIS H 57 ASP H 102 SER H 195 SITE 1 AC1 12 HIS H 57 ASN H 98 LEU H 99 ILE H 174 SITE 2 AC1 12 ASP H 189 ALA H 190 SER H 195 TRP H 215 SITE 3 AC1 12 GLY H 216 GLY H 219 HOH H 264 HOH H 270 SITE 1 AC2 15 LYS H 36 GLN H 38 ARG H 73 THR H 74 SITE 2 AC2 15 ARG H 75 TYR H 76 ILE H 82 MET H 84 SITE 3 AC2 15 LYS H 236 GLN H 239 HOH H 282 HOH I 16 SITE 4 AC2 15 HOH I 17 HOH I 19 HOH I 22
CRYST1 90.800 90.800 132.500 90.00 90.00 90.00 P 43 21 2 8
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 0.011013 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011013 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007547 0.00000