HEADER HYDROLASE/HYDROLASE INHIBITOR 24-AUG-92 1ABJ TITLE STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' TITLE 2 SUBSITES OF SUBSTRATES AND INHIBITORS CAVEAT 1ABJ THE OG SER H 195 - C2 0G6 BOND AND THE NE2 HIS H 57 - C3 0G6 CAVEAT 2 1ABJ BOND ARE OUTSIDE ACCEPTED RANGE 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 ORGAN: PLASMA KEYWDS SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.QIU,A.TULINSKY REVDAT 4 13-JUL-11 1ABJ 1 VERSN REVDAT 3 24-FEB-09 1ABJ 1 VERSN REVDAT 2 01-APR-03 1ABJ 1 JRNL REVDAT 1 31-JAN-94 1ABJ 0 JRNL AUTH X.QIU,K.P.PADMANABHAN,V.E.CARPEROS,A.TULINSKY,T.KLINE, JRNL AUTH 2 J.M.MARAGANORE,J.W.FENTON 2ND. JRNL TITL STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF JRNL TITL 2 THE S' SUBSITES OF SUBSTRATES AND INHIBITORS. JRNL REF BIOCHEMISTRY V. 31 11689 1992 JRNL REFN ISSN 0006-2960 JRNL PMID 1445905 JRNL DOI 10.1021/BI00162A004 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.SKRZYPCZAK-JANKUN,V.CARPEROS,K.G.RAVICHANDRAN,A.TULINSKY, REMARK 1 AUTH 2 M.WESTBROOK,J.M.MARAGANORE REMARK 1 TITL STRUCTURE OF THE HIRUGEN AND HIRULOG 1 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,K.G.RAVICHANDRAN,A.TULINSKY,W.BODE,R.HUBER, REMARK 1 AUTH 2 C.ROITSCH,J.W.FENTON II REMARK 1 TITL THE STRUCTURE OF A COMPLEX OF RECOMBINANT HIRUDIN AND HUMAN REMARK 1 TITL 2 ALPHA-THROMBIN REMARK 1 REF SCIENCE V. 249 277 1990 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 3 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 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 + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 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 : 2305 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 196 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.017 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.600 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: REMARK 3 CAUTION SHOULD BE TAKEN IF SOLVENT MOLECULES WITH OCCUPANCY REMARK 3 LESS THAN 0.5 ARE USED IN ANY STRUCTURAL OR BIOLOGICAL REMARK 3 DISCUSSIONS. REMARK 4 REMARK 4 1ABJ 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 44.13000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.01000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 -5 REMARK 465 PHE L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 GLY L -1 REMARK 465 GLU L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 GLU H 247 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 1.92 REMARK 500 OG SER H 195 O2 0G6 H 1 1.99 REMARK 500 OG SER H 195 C3 0G6 H 1 2.09 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 SER H 214 CA SER H 214 CB 0.101 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. = -6.7 DEGREES REMARK 500 LEU L 3 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG L 4 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG L 14D NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU L 14G CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 SER H 27 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG H 35 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 HIS H 57 N - CA - CB ANGL. DEV. = 13.1 DEGREES REMARK 500 TYR H 60A CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP H 60E CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 VAL H 66 CB - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG H 73 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG H 73 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG H 101 CD - NE - CZ ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 LYS H 110 N - CA - CB ANGL. DEV. = 12.7 DEGREES REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP H 125 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 GLU H 127 OE1 - CD - OE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG H 137 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG H 137 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 THR H 149 N - CA - CB ANGL. DEV. = 15.1 DEGREES REMARK 500 GLU H 164 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG H 175 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 GLU H 186B OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG H 187 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG H 187 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 CYS H 191 CA - CB - SG ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG H 221A NH1 - CZ - NH2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG H 221A NE - CZ - NH2 ANGL. DEV. = -8.6 DEGREES REMARK 500 TYR H 228 C - N - CA ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG H 233 CD - NE - CZ ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG H 233 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 LYS H 235 CA - CB - CG ANGL. DEV. = 22.3 DEGREES REMARK 500 ASP H 243 CB - CG - OD2 ANGL. DEV. = 8.5 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 ASP L 1A -0.26 -151.37 REMARK 500 PHE L 7 -70.54 -126.50 REMARK 500 LYS L 14A -9.97 -59.26 REMARK 500 THR L 14B 29.50 -148.57 REMARK 500 SER H 36A 123.74 -170.94 REMARK 500 SER H 48 -178.41 174.42 REMARK 500 TYR H 60A 88.06 -154.38 REMARK 500 ASN H 60G 74.65 -161.24 REMARK 500 HIS H 71 -64.98 -128.55 REMARK 500 ARG H 77A -75.51 -36.00 REMARK 500 ILE H 79 -62.18 -96.18 REMARK 500 GLU H 97A -71.61 -121.72 REMARK 500 ARG H 101 59.07 73.66 REMARK 500 ASP H 189 172.51 175.82 REMARK 500 SER H 195 146.68 -39.34 REMARK 500 SER H 214 -70.77 -112.83 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 0.16 SIDE CHAIN REMARK 500 ARG H 126 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG H 77A 22.4 L L OUTSIDE RANGE 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 457 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH H 508 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH H 520 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH H 529 DISTANCE = 8.23 ANGSTROMS REMARK 525 HOH H 539 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH H 542 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH H 546 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH H 565 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH H 566 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH H 571 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH H 580 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH H 587 DISTANCE = 5.08 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE REMARK 600 UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. REMARK 600 UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A REMARK 600 COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT REMARK 600 BOND TO NE2 OF HIS 57 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE 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 0G6 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G6 H 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSIN NUMBERING SYSTEM IS USED FOR THROMBIN, BASED REMARK 999 ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF REMARK 999 CHYMOTRYPSIN (BODE, W., ET AL., 1989, EMBO J. 8, 3467 - REMARK 999 3475). DBREF 1ABJ L -5 17 UNP P00734 THRB_HUMAN 328 363 DBREF 1ABJ H 16 247 UNP P00734 THRB_HUMAN 364 622 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 HET 0G6 H 1 30 HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETSYN 0G6 PPACK FORMUL 3 0G6 C21 H34 CL N6 O3 1+ FORMUL 4 HOH *196(H2 O) HELIX 1 1 THR L 14B GLU L 14H 1 7 HELIX 2 2 ALA H 55 CYS H 58 5 4 HELIX 3 3 PRO H 60B ASP H 60E 5 4 HELIX 4 4 THR H 60I ASN H 62 5 3 HELIX 5 5 ASP H 125 LEU H 130 1 9 HELIX 6 6 GLU H 164 SER H 171 1 8 HELIX 7 7 VAL H 231 ASP H 243 1 13 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 N VAL H 157 O SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 A 7 TRP H 207 TRP H 215 -1 N TYR H 208 O MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214 SHEET 7 A 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 B 7 GLN H 30 ARG H 35 0 SHEET 2 B 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 B 7 TRP H 51 THR H 54 -1 N LEU H 53 O SER H 45 SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 B 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 B 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85 SHEET 7 B 7 GLN H 30 ARG H 35 -1 N MET H 32 O ARG H 67 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.05 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 LINK C2 0G6 H 1 OG SER H 195 1555 1555 1.82 LINK C3 0G6 H 1 NE2 HIS H 57 1555 1555 1.89 CISPEP 1 SER H 36A PRO H 37 0 -2.73 SITE 1 AC1 19 HIS H 57 GLU H 97A LEU H 99 ILE H 174 SITE 2 AC1 19 ASP H 189 ALA H 190 CYS H 191 GLY H 193 SITE 3 AC1 19 SER H 195 SER H 214 TRP H 215 GLY H 216 SITE 4 AC1 19 GLY H 219 GLY H 226 ASP H 243 GLN H 244 SITE 5 AC1 19 HOH H 408 HOH H 409 HOH H 460 CRYST1 88.260 68.020 61.220 90.00 90.00 90.00 P 21 21 21 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 0.011330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016335 0.00000