HEADER HYDROLASE/HYDROLASE INHIBITOR 26-MAY-94 1TMT TITLE CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND HUMAN TITLE 2 ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS 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: CGP 50,856 INHIBITOR, CLEAVED N-TERMINAL TRIPEPTIDE COMPND 13 FRAGMENT, D-PHE-PRO-ARG; COMPND 14 CHAIN: I; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: CGP 50,856 INHIBITOR, CLEAVED C-TERMINAL HIRUDIN FRAGMENT; COMPND 18 CHAIN: J; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 MOL_ID: 4 KEYWDS COMPLEX, SERINE PROTEASE, INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.P.PRIESTLE,M.G.GRUETTER REVDAT 9 16-OCT-24 1TMT 1 REMARK REVDAT 8 21-DEC-22 1TMT 1 SEQADV HETSYN REVDAT 7 29-JUL-20 1TMT 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE REVDAT 6 29-NOV-17 1TMT 1 HELIX REVDAT 5 09-NOV-16 1TMT 1 REMARK REVDAT 4 13-JUL-11 1TMT 1 VERSN REVDAT 3 24-FEB-09 1TMT 1 VERSN REVDAT 2 01-APR-03 1TMT 1 JRNL REVDAT 1 30-SEP-94 1TMT 0 JRNL AUTH J.P.PRIESTLE,J.RAHUEL,H.RINK,M.TONES,M.G.GRUTTER JRNL TITL CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES JRNL TITL 2 AND HUMAN ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS. JRNL REF PROTEIN SCI. V. 2 1630 1993 JRNL REFN ISSN 0961-8368 JRNL PMID 8251938 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.SKRZYPCZAK-JANKUN,V.E.CARPEROS,K.G.RAVICHANDRAN,A.TULINSKY REMARK 1 TITL STRUCTURE OF THE HIRUGEN AND HIRULOG COMPLEXES OF REMARK 1 TITL 2 ALPHA-THROMBIN REMARK 1 REF J.MOL.BIOL. V. 221 1379 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.J.RYDEL,A.TULINSKY,W.BODE,R.HUBER REMARK 1 TITL REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX REMARK 1 REF J.MOL.BIOL. V. 221 583 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.G.GRUETTER,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 REFERENCE 4 REMARK 1 AUTH W.BODE,I.MAYR,U.BAUMANN,R.HUBER,S.R.STONE,J.HOFSTEENGE REMARK 1 TITL THE REFINED 1.9 ANGSTROM CRYSTAL STRUCTURE OF HUMAN ALPHA REMARK 1 TITL 2 THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE REMARK 1 TITL 3 AND 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 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 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 : 2401 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 111 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) : 0.014 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 3.000 ; 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: NULL REMARK 4 REMARK 4 1TMT 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_1000176737. 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) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 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 (%): 54.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 40.25000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.55000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I, J 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 RESIDUE DPN I 1 OF INHIBITOR CGP 50,856 IS A D-PHE. REMARK 400 REMARK 400 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. REMARK 400 CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 REMARK 400 CHAIN IDENTIFIER *H* IS USED FOR RESIDUES 16 - 247. REMARK 400 THE CGP 50,856 INHIBITOR IS BELIEVED TO BE CLEAVED AFTER REMARK 400 THE THIRD RESIDUE BASED ON THE ELECTRON DENSITY MAPS. REMARK 400 CHAIN IDENTIFIER *I* IS USED FOR THE FIRST THREE RESIDUES REMARK 400 OF THE CGP 50,856 INHIBITOR. CHAIN IDENTIFIER *J* IS USED REMARK 400 FOR THE REMAINING 18 RESIDUES OF THE CGP 50,856 INHIBITOR. REMARK 400 REMARK 400 THE BIVALIRUDIN C-TERMINUS FRAGMENT IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 THROMBIN INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BIVALIRUDIN C-TERMINUS FRAGMENT REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 GLU L 1C REMARK 465 ASP L 14L REMARK 465 GLY L 14M REMARK 465 ARG L 15 REMARK 465 GLU H 247 REMARK 465 PRO J 48 REMARK 465 GLY J 49 REMARK 465 GLY J 50 REMARK 465 GLY J 51 REMARK 465 GLY J 52 REMARK 465 ASP J 53 REMARK 465 GLY J 54 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 ILE L 14K CA C O CB CG1 CG2 CD1 REMARK 470 LYS H 81 CD CE NZ REMARK 470 LYS H 110 CE NZ REMARK 470 LYS H 149E CG CD CE NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 GLY H 246 CA C O REMARK 470 ASP J 55 CG OD1 OD2 REMARK 470 GLN J 65 CA C O CB CG CD OE1 REMARK 470 GLN J 65 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CG ASN H 60G C1 NAG J 301 2.13 REMARK 500 ND2 ASN H 60G O5 NAG J 301 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 14H CD GLU L 14H OE1 0.067 REMARK 500 GLU H 80 CD GLU H 80 OE1 0.071 REMARK 500 GLU H 127 CD GLU H 127 OE2 0.077 REMARK 500 GLU J 58 CD GLU J 58 OE1 0.072 REMARK 500 GLU J 62 CD GLU J 62 OE1 0.067 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 H 49 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP H 60E CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP H 63 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP H 63 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP H 100 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP H 100 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR H 117 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG H 175 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG H 175 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP H 178 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP H 178 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP H 186A CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP H 189 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP H 194 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 TYR H 208 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP H 222 CB - CG - OD1 ANGL. DEV. = -5.4 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 PHE L 7 -94.60 -122.37 REMARK 500 PRO H 28 1.11 -60.98 REMARK 500 SER H 48 -179.31 -175.28 REMARK 500 TYR H 60A 82.30 -156.24 REMARK 500 ASP H 60E 31.94 71.77 REMARK 500 ASN H 60G 68.85 -151.43 REMARK 500 HIS H 71 -54.07 -131.81 REMARK 500 ASN H 98 16.74 -143.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 RESIDUE TYR J 63 OF INHIBITOR CGP 50,856 REMARK 600 IS NOT SULFATED AS IT IS IN NATIVE HIRUDIN. REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET PRESENTED AS *BS1* ON SHEET RECORDS BELOW IS REMARK 700 ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED REMARK 700 BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST REMARK 700 STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *BS2* ON REMARK 700 SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA- REMARK 700 BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED SHEET IN REMARK 700 WHICH THE FIRST AND SECOND TO LAST STRANDS ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD OF THROMBIN REMARK 800 REMARK 800 SITE_IDENTIFIER: S3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SUBSITE 3 ON THROMBIN REMARK 800 REMARK 800 SITE_IDENTIFIER: S2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SUBSITE 2 ON THROMBIN REMARK 800 REMARK 800 SITE_IDENTIFIER: S1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SUBSITE 1 ON THROMBIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) REMARK 999 SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT REMARK 999 WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., REMARK 999 1989, EMBO J. 8, 3467-3475). REMARK 999 2. THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. REMARK 999 CHAIN ID *L* IS USED FOR RESIDUES 1H - 15 REMARK 999 CHAIN ID *H* IS USED FOR RESIDUES 16 - 247. REMARK 999 3. THE CGP 50,856 INHIBITOR IS BELIEVED TO BE CLEAVED REMARK 999 AFTER THE THIRD RESIDUE BASED ON THE ELECTRON DENSITY REMARK 999 MAPS. CHAIN IDENTIFIER *I* IS USED FOR THE FIRST THREE REMARK 999 RESIDUES OF THE CGP 50,856 INHIBITOR. REMARK 999 CHAIN IDENTIFIER *J* IS USED FOR THE REMAINING 18 REMARK 999 RESIDUES OF THE CGP 50,856 INHIBITOR. DBREF 1TMT L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1TMT H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1TMT I 1 3 PDB 1TMT 1TMT 1 3 DBREF 1TMT J 53 65 UNP P28504 HIR2_HIRME 53 65 SEQADV 1TMT PRO J 48 UNP P28504 LINKER SEQADV 1TMT GLY J 49 UNP P28504 LINKER SEQADV 1TMT GLY J 50 UNP P28504 LINKER SEQADV 1TMT GLY J 51 UNP P28504 LINKER SEQADV 1TMT GLY J 52 UNP P28504 LINKER 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 3 DPN PRO ARG SEQRES 1 J 18 PRO GLY GLY GLY GLY ASP GLY ASP PHE GLU GLU ILE PRO SEQRES 2 J 18 GLU GLU TYR LEU GLN MODRES 1TMT ASN H 60G ASN GLYCOSYLATION SITE HET DPN I 1 11 HET NAG J 301 14 HETNAM DPN D-PHENYLALANINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 DPN C9 H11 N O2 FORMUL 5 NAG C8 H15 N O6 FORMUL 6 HOH *111(H2 O) HELIX 1 AH1 ARG L 4 SER L 11 1MIXED ALPHA, 3/10 8 HELIX 2 AH2 THR L 14B TYR L 14J 1MIXED ALPHA, 3/10 9 HELIX 3 BH1 ASP H 125 LEU H 130 1 9 HELIX 4 BH2 GLU H 164 SER H 171 1 8 HELIX 5 BH3 LEU H 234 PHE H 245 1 12 HELIX 6 HH1 PRO J 60 LEU J 64 5 5 SHEET 1 BS1 7 TRP H 29 LYS H 36 0 SHEET 2 BS1 7 GLU H 39 ILE H 47 -1 N ALA H 44 O VAL H 31 SHEET 3 BS1 7 ARG H 50 THR H 54 -1 N LEU H 53 O SER H 45 SHEET 4 BS1 7 ILE H 103 LYS H 109 -1 N MET H 106 O VAL H 52 SHEET 5 BS1 7 LYS H 81 HIS H 91 -1 N TYR H 89 O LEU H 105 SHEET 6 BS1 7 ASP H 63 ILE H 68 -1 N VAL H 66 O SER H 83 SHEET 7 BS1 7 TRP H 29 LYS H 36 -1 N PHE H 34 O LEU H 65 SHEET 1 BS2 8 LEU H 155 VAL H 163 0 SHEET 2 BS2 8 ASN H 179 GLY H 184 -1 N GLY H 184 O PRO H 161 SHEET 3 BS2 8 GLY H 226 VAL H 231 -1 N TYR H 228 O PHE H 181 SHEET 4 BS2 8 ASN H 204B TRP H 215 -1 N ILE H 212 O THR H 229 SHEET 5 BS2 8 GLY H 196 SER H 203 -1 N MET H 201 O TYR H 208 SHEET 6 BS2 8 GLY H 133 GLY H 140 -1 N ARG H 137 O VAL H 200 SHEET 7 BS2 8 LEU H 155 VAL H 163 -1 N VAL H 158 O VAL H 138 SHEET 8 BS2 8 SER H 20 ALA H 22 -1 N SER H 20 O VAL H 157 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.00 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.00 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK ND2 ASN H 60G C1 NAG J 301 1555 1555 1.31 LINK C DPN I 1 N PRO I 2 1555 1555 1.38 CISPEP 1 SER H 36A PRO H 37 0 -1.19 SITE 1 CAT 3 SER H 195 HIS H 57 ASP H 102 SITE 1 S3 5 GLU H 97A ASN H 98 LEU H 99 TRP H 215 SITE 2 S3 5 GLY H 216 SITE 1 S2 5 HIS H 57 TYR H 60A LEU H 99 GLU H 192 SITE 2 S2 5 SER H 214 SITE 1 S1 10 HIS H 57 ASP H 189 ALA H 190 CYS H 191 SITE 2 S1 10 SER H 195 TRP H 215 GLY H 216 GLY H 219 SITE 3 S1 10 CYS H 220 GLY H 226 CRYST1 80.500 107.100 45.800 90.00 90.00 90.00 P 21 21 2 4 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 0.012422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021834 0.00000