PDB Short entry for 1A4W HEADER HYDROLASE/HYDROLASE INHIBITOR 06-FEB-98 1A4W TITLE CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: TITLE 2 PROBES OF THE S1' BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-THROMBIN (SMALL SUBUNIT); COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ALPHA-THROMBIN (LARGE SUBUNIT); COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIRUGEN; COMPND 11 CHAIN: I; COMPND 12 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: BLOOD; SOURCE 6 TISSUE: BLOOD; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 ORGAN: BLOOD; SOURCE 12 TISSUE: BLOOD; SOURCE 13 MOL_ID: 3 KEYWDS SERINE PROTEASE-INHIBITOR, BLOOD COAGULATION, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,A.TULINSKY REVDAT 4 02-AUG-23 1A4W 1 COMPND REMARK HETNAM LINK REVDAT 3 13-JUL-11 1A4W 1 VERSN REVDAT 2 24-FEB-09 1A4W 1 VERSN REVDAT 1 29-APR-98 1A4W 0 JRNL AUTH J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF, JRNL AUTH 2 A.TULINSKY JRNL TITL CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING JRNL TITL 2 INHIBITORS: PROBES OF THE S1' BINDING SITE. JRNL REF BIOPHYS.J. V. 71 2830 1996 JRNL REFN ISSN 0006-3495 JRNL PMID 8913620 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.VIJAYALAKSHMI,K.P.PADMANABHAN,K.G.MANN,A.TULINSKY REMARK 1 TITL THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-, AND REMARK 1 TITL 2 PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE REMARK 1 TITL 3 BINDING TO THROMBIN REMARK 1 REF PROTEIN SCI. V. 3 2254 1994 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.TULINSKY,X.QIU REMARK 1 TITL ACTIVE SITE AND EXOSITE BINDING OF ALPHA-THROMBIN REMARK 1 REF BLOOD COAGULATION V. 4 305 1993 REMARK 1 REF 2 FIBRINOLYSIS REMARK 1 REFN ISSN 0957-5235 REMARK 1 REFERENCE 3 REMARK 1 AUTH X.QIU,K.P.PADMANABHAN,V.E.CARPEROS,A.TULINSKY,T.KLINE, REMARK 1 AUTH 2 J.M.MARAGANORE,J.W.FENTON II REMARK 1 TITL STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF REMARK 1 TITL 2 THE S' SUBSITES OF SUBSTRATES AND INHIBITORS REMARK 1 REF BIOCHEMISTRY V. 31 11689 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 65.0 REMARK 3 NUMBER OF REFLECTIONS : 19906 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.155 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 FIT/AGREEMENT OF MODEL WITH ALL DATA. 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 : 2238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; 0.015 REMARK 3 ANGLE DISTANCE (A) : 0.042 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.051 ; 0.045 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.032 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.210 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.190 ; 0.600 REMARK 3 MULTIPLE TORSION (A) : 0.210 ; 0.600 REMARK 3 H-BOND (X...Y) (A) : 0.250 ; 0.600 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.000 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 20.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 30.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.100 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.800 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.100 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A4W 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_1000170395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-94 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.5 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PREVIOUS STRUCTURE REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1FPC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM PHOSPHATE BUFFER AT PH REMARK 280 7.3, 27-28% PEG 8000; HANGING DROPS WITH MACROSEEDING, VAPOR REMARK 280 DIFFUSION - HANGING DROP AND MACROSEEDING REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 35.73500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.73500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.00000 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: TRIMERIC 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 IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN REMARK 400 IDENTIFIER *H* IS USED FOR RESIDUES 16 - 247. CHAIN REMARK 400 IDENTIFIER *I* IS USED FOR HIRUGEN, THE CARBOXYL. 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 ALA L 1B REMARK 465 ASP L 14L REMARK 465 GLY L 14M REMARK 465 ARG L 14N REMARK 465 THR H 146A REMARK 465 TRP H 146B REMARK 465 THR H 146C REMARK 465 ALA H 146D REMARK 465 ASN H 146E REMARK 465 VAL H 146F REMARK 465 GLY H 146G REMARK 465 LYS H 146H REMARK 465 PHE H 245 REMARK 465 GLY H 246 REMARK 465 GLU H 247 REMARK 465 ASN I 353 REMARK 465 GLY I 354 REMARK 465 LEU I 364 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 LYS L 14A CG CD CE NZ REMARK 470 ARG L 14D CG CD NE CZ NH1 NH2 REMARK 470 ILE L 14K CB CG1 CG2 CD1 REMARK 470 ASN H 62 CB CG OD1 ND2 REMARK 470 ARG H 75 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG H 77A CB CG CD NE CZ NH1 NH2 REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 ASP H 125 CG OD1 OD2 REMARK 470 LYS H 145 CG CD CE NZ REMARK 470 ASP H 186A CB CG OD1 OD2 REMARK 470 LYS H 240 CD CE NZ REMARK 470 GLN H 244 CB CG CD OE1 NE2 REMARK 470 ASP I 355 CB CG OD1 OD2 REMARK 470 GLU I 358 CB CG CD OE1 OE2 REMARK 470 GLU I 361 CG CD OE1 OE2 REMARK 470 GLU I 362 CG CD OE1 OE2 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 NH1 ARG H 50 O LEU H 108 1.96 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 1A CB - CG - OD1 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 SER L 11 N - CA - CB ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU L 14G CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP H 21 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG H 35 NH1 - CZ - NH2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG H 50 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TYR H 60A CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 LYS H 60F CA - CB - CG ANGL. DEV. = 17.9 DEGREES REMARK 500 LEU H 64 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG H 73 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG H 73 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 THR H 74 N - CA - CB ANGL. DEV. = -17.7 DEGREES REMARK 500 THR H 74 OG1 - CB - CG2 ANGL. DEV. = 18.9 DEGREES REMARK 500 SER H 83 N - CA - CB ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG H 93 CD - NE - CZ ANGL. DEV. = 20.6 DEGREES REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG H 93 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR H 94 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP H 100 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ASP H 102 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG H 137 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 VAL H 138 O - C - N ANGL. DEV. = 11.8 DEGREES REMARK 500 VAL H 154 CA - CB - CG1 ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG H 165 CD - NE - CZ ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG H 165 NE - CZ - NH1 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG H 165 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP H 170 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG H 173 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR H 184A CB - CG - CD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 GLU H 186B CG - CD - OE1 ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR H 208 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 TYR H 228 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 PHE H 232 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG H 233 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG H 233 NE - CZ - NH2 ANGL. DEV. = -9.4 DEGREES REMARK 500 VAL H 241 CA - CB - CG1 ANGL. DEV. = 12.4 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 -78.63 -128.28 REMARK 500 SER H 36A 117.15 -163.62 REMARK 500 ALA H 44 -175.78 -171.19 REMARK 500 TYR H 60A 79.88 -154.74 REMARK 500 ASN H 60G 83.28 -160.79 REMARK 500 HIS H 71 -56.01 -134.72 REMARK 500 ASN H 78 -0.86 71.84 REMARK 500 GLU H 97A -63.15 -131.02 REMARK 500 LYS H 186D 143.14 179.93 REMARK 500 SER H 214 -98.33 -112.77 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 73 0.12 SIDE CHAIN REMARK 500 PHE H 232 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER H 20 11.04 REMARK 500 GLN H 151 10.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 542 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 85.2 REMARK 620 3 PHE H 204A O 97.8 93.6 REMARK 620 4 HOH H 467 O 171.9 94.2 90.3 REMARK 620 5 HOH H 515 O 74.9 84.0 172.5 97.0 REMARK 620 6 HOH H 518 O 84.9 166.5 78.7 96.9 102.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 541 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 95.7 REMARK 620 3 HOH H 403 O 87.1 90.7 REMARK 620 4 HOH H 460 O 160.8 71.0 79.4 REMARK 620 5 HOH H 464 O 98.3 165.3 86.0 94.3 REMARK 620 6 HOH H 497 O 104.9 92.4 167.3 89.9 87.9 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: AMINO{[(4S)-4-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL] REMARK 630 SULFONYL}AMINO)-5-OXO-5-{(2R)-2-[3-OXO-3-(1,3-THIAZOL-2-YL)PROPYL] REMARK 630 PIP ERIDIN-1-YL}PENTYL]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 QWE H 373 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ANS ARG 5TP REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 541 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 542 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QWE H 373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUGEN DBREF 1A4W L 1H 14N UNP P00734 THRB_HUMAN 328 363 DBREF 1A4W H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1A4W I 353 364 UNP P09945 ITH3_HIRME 60 71 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 12 ASN GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU MODRES 1A4W TYS I 363 TYR O-SULFO-L-TYROSINE HET TYS I 363 16 HET NA H 541 1 HET NA H 542 1 HET QWE H 373 42 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM QWE AMINO{[(4S)-4-({[5-(DIMETHYLAMINO)NAPHTHALEN-1- HETNAM 2 QWE YL]SULFONYL}AMINO)-5-OXO-5-{(2R)-2-[3-OXO-3-(1,3- HETNAM 3 QWE THIAZOL-2-YL)PROPYL]PIP ERIDIN-1- HETNAM 4 QWE YL}PENTYL]AMINO}METHANIMINIUM HETSYN QWE RWJ-50215 FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 QWE C29 H40 N7 O4 S2 1+ FORMUL 7 HOH *157(H2 O) HELIX 1 H1 ALA H 55 LEU H 60 1 6 HELIX 2 H2 GLU H 164 SER H 171 1 8 HELIX 3 H3 ASP H 125 LEU H 129C 1 8 HELIX 4 H4 VAL H 231 GLN H 244 1 14 SHEET 1 B1 7 PRO H 28 ARG H 35 0 SHEET 2 B1 7 CYS H 42 ASP H 49 -1 SHEET 3 B1 7 ARG H 50 ALA H 56 -1 SHEET 4 B1 7 ARG H 101 LYS H 110 -1 SHEET 5 B1 7 LYS H 81 PRO H 92 -1 SHEET 6 B1 7 ASP H 63 GLY H 69 -1 SHEET 7 B1 7 PRO H 28 ARG H 35 -1 SHEET 1 B2 7 GLY H 133 TRP H 141 0 SHEET 2 B2 7 LEU H 155 ILE H 162 -1 SHEET 3 B2 7 ASN H 179 PRO H 186 -1 SHEET 4 B2 7 GLY H 223 THR H 229 -1 SHEET 5 B2 7 ILE H 212 GLU H 217 -1 SHEET 6 B2 7 GLY H 193 MET H 201 -1 SHEET 7 B2 7 GLY H 133 TRP H 141 -1 SSBOND 1 CYS L 1 CYS H 122 1555 1555 1.97 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.06 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.09 LINK C GLU I 362 N TYS I 363 1555 1555 1.33 LINK O LYS H 169 NA NA H 542 1555 1555 2.36 LINK O THR H 172 NA NA H 542 1555 1555 2.33 LINK O PHE H 204A NA NA H 542 4546 1555 2.43 LINK O ARG H 221A NA NA H 541 1555 1555 2.44 LINK O LYS H 224 NA NA H 541 1555 1555 2.32 LINK O HOH H 403 NA NA H 541 1555 1555 2.91 LINK O HOH H 460 NA NA H 541 1555 1555 2.41 LINK O HOH H 464 NA NA H 541 1555 1555 2.37 LINK O HOH H 467 NA NA H 542 1555 1555 2.39 LINK O HOH H 497 NA NA H 541 1555 1555 2.21 LINK O HOH H 515 NA NA H 542 1555 1555 2.84 LINK O HOH H 518 NA NA H 542 1555 1555 2.54 CISPEP 1 SER H 36A PRO H 37 0 -2.26 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H 403 HOH H 460 SITE 2 AC1 6 HOH H 464 HOH H 497 SITE 1 AC2 6 LYS H 169 THR H 172 PHE H 204A HOH H 467 SITE 2 AC2 6 HOH H 515 HOH H 518 SITE 1 AC3 14 HIS H 57 TYR H 60A TRP H 60D LYS H 60F SITE 2 AC3 14 GLU H 97A LEU H 99 ASP H 189 ALA H 190 SITE 3 AC3 14 TRP H 215 GLY H 216 GLY H 219 HOH H 448 SITE 4 AC3 14 HOH H 471 HOH H 532 SITE 1 AC4 14 PHE H 34 ARG H 67 ARG H 73 THR H 74 SITE 2 AC4 14 ARG H 75 TYR H 76 LYS H 81 ILE H 82 SITE 3 AC4 14 HOH H 393 HOH H 432 HOH I 419 HOH I 435 SITE 4 AC4 14 HOH I 476 HOH I 504 CRYST1 71.470 72.000 73.390 90.00 101.13 90.00 C 1 2 1 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 0.013992 0.000000 0.002753 0.00000 SCALE2 0.000000 0.013889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013887 0.00000