HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JUL-92 1ETS 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 1ETS 1 VERSN REVDAT 4 25-AUG-09 1ETS 1 SOURCE REVDAT 3 24-FEB-09 1ETS 1 VERSN REVDAT 2 01-APR-03 1ETS 1 JRNL REVDAT 1 31-JAN-94 1ETS 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. 2.30 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) : 2.30 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) : 0.178 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 : 37 REMARK 3 SOLVENT ATOMS : 228 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 3.09 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 1ETS 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 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 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 (%): 56.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 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 44.36500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.45000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.36500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.36500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.36500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.36500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.45000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.36500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.36500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.45000 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: 2570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 ILE L 14K 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 119 NE2 HIS H 119 CD2 -0.072 REMARK 500 HIS H 131 NE2 HIS H 131 CD2 -0.076 REMARK 500 HIS H 230 NE2 HIS H 230 CD2 -0.077 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 ARG L 4 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 THR L 14B CA - CB - CG2 ANGL. DEV. = -9.9 DEGREES REMARK 500 TYR L 14J CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TRP H 51 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP H 51 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP H 60D CD1 - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TRP H 60D CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 VAL H 61 CG1 - CB - CG2 ANGL. DEV. = -12.9 DEGREES REMARK 500 TYR H 89 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP H 96 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP H 96 CB - CG - CD1 ANGL. DEV. = -8.5 DEGREES REMARK 500 TRP H 96 CE2 - CD2 - CG ANGL. DEV. = -6.5 DEGREES REMARK 500 LEU H 105 CB - CG - CD2 ANGL. DEV. = -12.2 DEGREES REMARK 500 TRP H 141 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP H 141 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG H 144 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG H 145 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 TRP H 148 CD1 - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP H 148 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP H 148 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP H 148 CG - CD2 - CE3 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG H 175 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 CYS H 182 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG H 187 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TRP H 207 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP H 207 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 TRP H 215 CD1 - CG - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP H 215 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 SER H 214 CA - C - N ANGL. DEV. = 15.9 DEGREES REMARK 500 TYR H 225 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 TYR H 225 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 TRP H 237 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP H 237 CG - CD1 - NE1 ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP H 237 CE2 - CD2 - CG 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 ALA L 1E -170.21 175.56 REMARK 500 ALA L 1B -122.79 -133.40 REMARK 500 PHE L 7 -92.29 -137.54 REMARK 500 GLN L 14A -65.34 -12.59 REMARK 500 TRP H 29 -6.46 -38.87 REMARK 500 LEU H 41 -60.35 -102.31 REMARK 500 ARG H 50 10.51 -152.12 REMARK 500 ASP H 60E 25.40 39.80 REMARK 500 HIS H 71 -54.95 -156.23 REMARK 500 LYS H 97 31.14 -91.08 REMARK 500 GLU H 97A -72.53 -169.15 REMARK 500 ASN H 98 26.26 -154.46 REMARK 500 ASP H 116 -23.78 -35.68 REMARK 500 ASN H 143 124.61 -24.18 REMARK 500 THR H 149 93.34 -67.29 REMARK 500 GLU H 149E -37.87 73.07 REMARK 500 VAL H 150 30.82 -75.23 REMARK 500 GLU H 186B 20.36 -75.38 REMARK 500 ASN H 205 33.35 72.96 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 VAL H 79 GLU H 80 -143.26 REMARK 500 PRO H 198 PHE H 199 143.62 REMARK 500 LEU H 245 GLY H 246 -148.62 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 ARG H 187 0.10 SIDE CHAIN REMARK 500 TYR H 225 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 505 DISTANCE = 10.36 ANGSTROMS REMARK 525 HOH H 513 DISTANCE = 8.09 ANGSTROMS REMARK 525 HOH H 516 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH H 529 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH H 553 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH H 562 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH H 592 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH H 612 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH H 616 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH H 619 DISTANCE = 5.52 ANGSTROMS REMARK 525 HOH H 656 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH H 669 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH H 711 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH H 764 DISTANCE = 5.32 ANGSTROMS REMARK 525 HOH H 767 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH H 770 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH H 773 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH L 534 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH L 536 DISTANCE = 6.25 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 AMIDINOPHENYLALANINE (OF NAPAP) BINDS TO S1 SPECIFICITY REMARK 600 POCKET, PIPERIDINE TO S2 AND NAPHLYL GROUP TO "ARYL REMARK 600 BINDING SITE". 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 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 MID H 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ETR 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 1ETS L -12 15 UNP P00735 THRB_BOVIN 318 366 DBREF 1ETS 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 MID H 1 43 HETNAM MID 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4-CARBAMIMIDOYL-D- HETNAM 2 MID PHENYLALANYL]PIPERIDINE HETSYN MID NAPAP FORMUL 3 MID C27 H31 N5 O4 S FORMUL 4 HOH *228(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 2.03 SSBOND 2 CYS H 42 CYS H 58 1555 1555 1.99 SSBOND 3 CYS H 168 CYS H 182 1555 1555 1.89 SSBOND 4 CYS H 191 CYS H 220 1555 1555 1.91 CISPEP 1 SER H 36A PRO H 37 0 -8.21 SITE 1 AC1 14 HIS H 57 TRP H 60D ASN H 98 LEU H 99 SITE 2 AC1 14 ASP H 189 ALA H 190 GLU H 192 SER H 195 SITE 3 AC1 14 SER H 214 TRP H 215 GLY H 216 GLU H 217 SITE 4 AC1 14 GLY H 219 HOH H 576 CRYST1 88.730 88.730 102.900 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 0.011270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009718 0.00000