HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JUL-92 1ETR
TITLE REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN
TITLE 2 COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN
TITLE 3 INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING
TITLE 4 ANTITHROMBOTICS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: EPSILON-THROMBIN;
COMPND 3 CHAIN: L;
COMPND 4 EC: 3.4.21.5;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: EPSILON-THROMBIN;
COMPND 8 CHAIN: H;
COMPND 9 EC: 3.4.21.5;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: COW;
SOURCE 4 ORGANISM_TAXID: 9913;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 7 ORGANISM_COMMON: COW;
SOURCE 8 ORGANISM_TAXID: 9913
KEYWDS SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR W.BODE,H.BRANDSTETTER
REVDAT 5 13-JUL-11 1ETR 1 VERSN
REVDAT 4 25-AUG-09 1ETR 1 SOURCE
REVDAT 3 24-FEB-09 1ETR 1 VERSN
REVDAT 2 01-APR-03 1ETR 1 JRNL
REVDAT 1 31-JAN-94 1ETR 0
JRNL AUTH H.BRANDSTETTER,D.TURK,H.W.HOEFFKEN,D.GROSSE,J.STURZEBECHER,
JRNL AUTH 2 P.D.MARTIN,B.F.EDWARDS,W.BODE
JRNL TITL REFINED 2.3 A X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN
JRNL TITL 2 COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED
JRNL TITL 3 THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA. A STARTING
JRNL TITL 4 POINT FOR IMPROVING ANTITHROMBOTICS.
JRNL REF J.MOL.BIOL. V. 226 1085 1992
JRNL REFN ISSN 0022-2836
JRNL PMID 1518046
JRNL DOI 10.1016/0022-2836(92)91054-S
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH W.BODE,H.BRANDSTETTER,D.TURK,M.BAUER,J.STUERZEBECHER
REMARK 1 TITL CRYSTALLOGRAPHIC DETERMINATION OF THROMBIN COMPLEXES WITH
REMARK 1 TITL 2 SMALL SYNTHETIC INHIBITORS AS A STARTING POINT FOR THE
REMARK 1 TITL 3 RECEPTOR-BASED DESIGN OF ANTITHROMBOTICS
REMARK 1 REF TO BE PUBLISHED
REMARK 1 REFN
REMARK 1 REFERENCE 2
REMARK 1 AUTH W.BODE
REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH
REMARK 1 TITL 2 D-PHE-PRO-ARG AND WITH SMALL BENZAMIDINE AND ARGININE-BASED
REMARK 1 TITL 3 "NON-PEPTIDIC" INHIBITORS
REMARK 1 REF TO BE PUBLISHED
REMARK 1 REFN
REMARK 1 REFERENCE 3
REMARK 1 AUTH W.BODE,D.TURK,A.KARSHIKOV
REMARK 1 TITL THE REFINED 1.9-ANGSTROMS X-RAY CRYSTAL STRUCTURE OF
REMARK 1 TITL 2 D-PHE-PRO-ARG CHLOROMETHYLKETONE-INHIBITED HUMAN
REMARK 1 TITL 3 ALPHA-THROMBIN: STRUCTURE ANALYSIS, OVERALL STRUCTURE,
REMARK 1 TITL 4 ELECTROSTATIC PROPERTIES, DETAILED ACTIVE-SITE GEOMETRY, AND
REMARK 1 TITL 5 STRUCTURE-FUNCTION RELATIONSHIPS
REMARK 1 REF PROTEIN SCI. V. 1 426 1992
REMARK 1 REFN ISSN 0961-8368
REMARK 1 REFERENCE 4
REMARK 1 AUTH D.TURK,J.STUERZEBECHER,W.BODE
REMARK 1 TITL GEOMETRY OF BINDING OF THE NALPHA-TOSYLATED PIPERIDIDES OF
REMARK 1 TITL 2 M-AMIDINO-, P-AMIDINO-AND P-GUANIDINO PHENYLALANINE TO
REMARK 1 TITL 3 THROMBIN AND TRYPSIN: X-RAY CRYSTAL STRUCTURES OF THEIR
REMARK 1 TITL 4 TRYPSIN COMPLEXES AND MODELING OF THEIR THROMBIN COMPLEXES
REMARK 1 REF FEBS LETT. V. 287 133 1991
REMARK 1 REFN ISSN 0014-5793
REMARK 1 REFERENCE 5
REMARK 1 AUTH W.BODE,D.TURK,J.STUERZEBECHER
REMARK 1 TITL GEOMETRY OF BINDING OF THE BENZAMIDINE-AND ARGININE-BASED
REMARK 1 TITL 2 INHIBITORS N-ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P-
REMARK 1 TITL 3 AMIDINOPHENYLALANYL-PIPERIDINE (NAPAP) AND
REMARK 1 TITL 4 (2R,4R)-4-METHYL-1-[N-ALPHA-(3-METHYL-1,2,3,4-TETRAHYDRO-8-
REMARK 1 TITL 5 QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC ACID
REMARK 1 TITL 6 (MQPA) TO HUMAN ALPHA-THROMBIN: X-RAY CRYSTALLOGRAPHIC
REMARK 1 TITL 7 DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF
REMARK 1 TITL 8 NAPAP-THROMBIN AND MQPA-THROMBIN
REMARK 1 REF EUR.J.BIOCHEM. V. 193 175 1990
REMARK 1 REFN ISSN 0014-2956
REMARK 1 REFERENCE 6
REMARK 1 AUTH W.BODE,I.MAYR,U.BAUMANN,R.HUBER,S.R.STONE,J.HOFSTEENGE
REMARK 1 TITL THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN
REMARK 1 TITL 2 ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG
REMARK 1 TITL 3 CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP
REMARK 1 TITL 4 INSERTION SEGMENT
REMARK 1 REF EMBO J. V. 8 3467 1989
REMARK 1 REFN ISSN 0261-4189
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.175
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 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2384
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 35
REMARK 3 SOLVENT ATOMS : 152
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.014
REMARK 3 BOND ANGLES (DEGREES) : 3.26
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN
REMARK 3 THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE
REMARK 3 THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS.
REMARK 3 NOTE THAT THE OCCUPANCY OF RESIDUES 148 - 149E IS GIVEN AS
REMARK 3 0.0 INDICATING THAT THEY WERE NOT SEEN IN THE ELECTRON
REMARK 3 DENSITY MAPS.
REMARK 4
REMARK 4 1ETR 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: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z
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 0.00000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.85500
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.85500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.49000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.85500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.85500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.49000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.85500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.85500
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.49000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.85500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.85500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.49000
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 0.00000
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13520 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H
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. (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 -12
REMARK 465 SER L -11
REMARK 465 GLU L -10
REMARK 465 ASP L -9
REMARK 465 HIS L -8
REMARK 465 PHE L -7
REMARK 465 GLN L -6
REMARK 465 PRO L -5
REMARK 465 PHE L -4
REMARK 465 PHE L -3
REMARK 465 ASN L -2
REMARK 465 GLU L -1
REMARK 465 LYS L 0
REMARK 475
REMARK 475 ZERO OCCUPANCY RESIDUES
REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY.
REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT
REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE)
REMARK 475 M RES C SSEQI
REMARK 475 THR L 1H
REMARK 475 PHE L 1G
REMARK 475 GLY L 1F
REMARK 475 ALA L 1E
REMARK 475 GLY L 1D
REMARK 475 GLU L 1C
REMARK 475 ALA L 1B
REMARK 475 ASP L 1A
REMARK 475 GLU L 14L
REMARK 475 GLY L 14M
REMARK 475 ARG L 15
REMARK 475 TRP H 148
REMARK 475 THR H 149
REMARK 475 THR H 149A
REMARK 475 SER H 149B
REMARK 475 VAL H 149C
REMARK 475 ALA H 149D
REMARK 475 GLU H 149E
REMARK 475 LYS H 236
REMARK 475 TRP H 237
REMARK 475 ILE H 238
REMARK 475 GLN H 239
REMARK 475 LYS H 240
REMARK 475 VAL H 241
REMARK 475 ILE H 242
REMARK 475 ASP H 243
REMARK 475 ARG H 244
REMARK 475 LEU H 245
REMARK 475 GLY H 246
REMARK 475 SER H 247
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 HIS H 131 NE2 HIS H 131 CD2 -0.068
REMARK 500 HIS H 230 NE2 HIS H 230 CD2 -0.075
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 TRP H 29 CD1 - CG - CD2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 TRP H 29 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES
REMARK 500 ARG H 35 CB - CG - CD ANGL. DEV. = -15.9 DEGREES
REMARK 500 TRP H 51 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES
REMARK 500 TRP H 51 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES
REMARK 500 TRP H 60D CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES
REMARK 500 TYR H 94 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 TYR H 94 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 TRP H 96 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES
REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 HIS H 131 CB - CG - CD2 ANGL. DEV. = -10.0 DEGREES
REMARK 500 TRP H 141 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES
REMARK 500 TRP H 141 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES
REMARK 500 ARG H 145 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 TRP H 148 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES
REMARK 500 TRP H 148 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES
REMARK 500 VAL H 157 CB - CA - C ANGL. DEV. = -14.2 DEGREES
REMARK 500 VAL H 157 CG1 - CB - CG2 ANGL. DEV. = 11.4 DEGREES
REMARK 500 VAL H 157 CA - CB - CG1 ANGL. DEV. = -9.3 DEGREES
REMARK 500 ARG H 165 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 TRP H 207 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 TRP H 207 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES
REMARK 500 TRP H 215 CD1 - CG - CD2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 TRP H 215 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 ARG H 221 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 TYR H 225 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 TYR H 228 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES
REMARK 500 TRP H 237 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 TRP H 237 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES
REMARK 500 LEU H 245 CA - CB - CG ANGL. DEV. = 14.4 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 ALA L 1E -46.49 69.79
REMARK 500 ALA L 1B -74.14 42.67
REMARK 500 PHE L 7 -81.39 -122.35
REMARK 500 GLN L 11 56.72 17.20
REMARK 500 PRO H 28 0.78 -68.45
REMARK 500 SER H 48 174.89 171.79
REMARK 500 ASP H 60E -2.95 53.64
REMARK 500 ASN H 60G 73.71 -157.33
REMARK 500 HIS H 71 -45.99 -131.75
REMARK 500 TYR H 76 108.65 -52.82
REMARK 500 TYR H 94 120.77 -36.32
REMARK 500 LYS H 97 47.99 -101.80
REMARK 500 GLU H 97A -86.87 175.24
REMARK 500 TRP H 148 -111.37 -103.04
REMARK 500 THR H 149A -140.68 -115.28
REMARK 500 ASP H 189 154.46 178.41
REMARK 500 CYS H 191 -159.46 -148.38
REMARK 500 ASN H 205 18.00 59.12
REMARK 500 SER H 214 -83.52 -104.68
REMARK 500 LYS H 240 -71.20 -47.10
REMARK 500 ARG H 244 -54.80 82.19
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 ASP H 63 LEU H 64 -146.39
REMARK 500 THR H 147 TRP H 148 144.76
REMARK 500 GLU H 149E VAL H 150 -140.30
REMARK 500 LEU H 245 GLY H 246 -124.54
REMARK 500 GLY H 246 SER H 247 140.05
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 TYR H 204A 0.07 SIDE CHAIN
REMARK 500 TYR H 225 0.12 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 THE ARGINYL SIDE-CHAIN OF INHIBITOR MQPA BINDS TO S1
REMARK 600 SPECIFICITY POCKET, PIPERIDINE TO S2 AND QUINOLINE TO
REMARK 600 "ARYL BINDING SITE".
REMARK 630
REMARK 630 MOLECULE TYPE: NULL
REMARK 630 MOLECULE NAME: AMINO{[(4S)-5-[(2R,4R)-2-CARBOXY-4-METHYLPIPERIDIN-
REMARK 630 1-YL]-4-({[(3R)-3-METHYL-1,2,3,4-TETRAHYDROQUINOLIN-8-YL]SULFONYL}
REMARK 630 AMINO)-5-OXOPENTYL]AMINO}METHANIMINIUM
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 MIT H 1
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: 34T ARG MCP
REMARK 630 DETAILS: NULL
REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS
REMARK 700 BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE
REMARK 700 REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND
REMARK 700 LAST STRANDS ARE IDENTICAL.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MIT H 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1ETS RELATED DB: PDB
REMARK 900 RELATED ID: 1ETT RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE NUMBERING OF THROMBIN RESIDUES IS BASED ON TOPOLOGICAL
REMARK 999 EQUIVALENCES WITH CHYMOTRYPSINOGEN.
DBREF 1ETR L -12 15 UNP P00735 THRB_BOVIN 318 366
DBREF 1ETR H 16 247 UNP P00735 THRB_BOVIN 367 625
SEQRES 1 L 49 THR SER GLU ASP HIS PHE GLN PRO PHE PHE ASN GLU LYS
SEQRES 2 L 49 THR PHE GLY ALA GLY GLU ALA ASP CYS GLY LEU ARG PRO
SEQRES 3 L 49 LEU PHE GLU LYS LYS GLN VAL GLN ASP GLN THR GLU LYS
SEQRES 4 L 49 GLU LEU PHE GLU SER TYR ILE GLU GLY ARG
SEQRES 1 H 259 ILE VAL GLU GLY GLN ASP ALA GLU VAL GLY LEU 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 VAL ASP ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG LYS VAL GLU LYS ILE
SEQRES 7 H 259 SER MET LEU ASP LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 H 259 TRP LYS GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS
SEQRES 9 H 259 LEU LYS ARG PRO ILE GLU LEU SER ASP TYR ILE HIS PRO
SEQRES 10 H 259 VAL CYS LEU PRO ASP LYS GLN THR ALA ALA LYS LEU LEU
SEQRES 11 H 259 HIS ALA GLY PHE LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 H 259 ARG ARG GLU THR TRP THR THR SER VAL ALA GLU VAL GLN
SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO LEU VAL GLU
SEQRES 14 H 259 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR
SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO GLY 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 TYR 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 ARG LEU GLY SER
HET MIT H 1 42
HETNAM MIT AMINO{[(4S)-5-[(2R,4R)-2-CARBOXY-4-METHYLPIPERIDIN-1-
HETNAM 2 MIT YL]-4-({[(3R)-3-METHYL-1,2,3,4-TETRAHYDROQUINOLIN-8-
HETNAM 3 MIT YL]SULFONYL}AMINO)-5-OXOPENTYL]AMINO}METHANIMINIUM
HETSYN MIT MQPA, MD-805; MITSUBISHI INHIBITOR
FORMUL 3 MIT C23 H37 N6 O5 S 1+
FORMUL 4 HOH *152(H2 O)
HELIX 1 1 GLU L 14C SER L 14I 13.6/13 7
HELIX 2 2 ALA H 55 LEU H 59 5 5
HELIX 3 3 TYR H 60A ASP H 60E 5 5
HELIX 4 4 ASP H 125 LEU H 129C 13.6/13 8
HELIX 5 5 GLU H 164 LYS H 169 13.6/13 6
HELIX 6 6 CYS H 168 THR H 172 5 5
HELIX 7 7 VAL H 231 LYS H 235 5 5
HELIX 8 8 LEU H 234 ASP H 243 13.6/13 10
SHEET 1 S1 7 LYS H 81 ASN H 95 0
SHEET 2 S1 7 ASP H 100 LYS H 109 -1
SHEET 3 S1 7 VAL H 52 THR H 54 -1
SHEET 4 S1 7 GLU H 39 LEU H 46 -1
SHEET 5 S1 7 TRP H 29 ARG H 35 -1
SHEET 6 S1 7 VAL H 66 ILE H 68 -1
SHEET 7 S1 7 LYS H 81 ASN H 95 -1
SHEET 1 S2 7 VAL H 150 LEU H 162 0
SHEET 2 S2 7 PHE H 134 ARG H 144 -1
SHEET 3 S2 7 PHE H 199 SER H 203 -1
SHEET 4 S2 7 ARG H 206 TRP H 215 -1
SHEET 5 S2 7 GLY H 226 THR H 229 -1
SHEET 6 S2 7 PHE H 181 ALA H 183 -1
SHEET 7 S2 7 VAL H 150 LEU H 162 -1
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.02
SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.01
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.05
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.00
CISPEP 1 SER H 36A PRO H 37 0 -3.57
SITE 1 AC1 13 HIS H 57 TYR H 60A LEU H 99 ASP H 189
SITE 2 AC1 13 ALA H 190 CYS H 191 SER H 195 TRP H 215
SITE 3 AC1 13 GLY H 216 GLY H 219 HOH H 561 HOH H 616
SITE 4 AC1 13 HOH H 632
CRYST1 87.710 87.710 102.980 90.00 90.00 90.00 P 42 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 0.011401 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011401 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009711 0.00000
(ATOM LINES ARE NOT SHOWN.)
END