HEADER HYDROLASE/HYDROLASE INHIBITOR 20-JUL-95 1DIT TITLE COMPLEX OF A DIVALENT INHIBITOR WITH THROMBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-THROMBIN; COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ALPHA-THROMBIN; COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PEPTIDE INHIBITOR CVS995; COMPND 11 CHAIN: P; 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 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3 KEYWDS HYDROLASE, BLOOD COAGULATION, INHIBITOR, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.TULINSKY,R.KRISHNAN REVDAT 4 15-NOV-23 1DIT 1 LINK ATOM REVDAT 3 13-JUL-11 1DIT 1 VERSN REVDAT 2 24-FEB-09 1DIT 1 VERSN REVDAT 1 10-JUN-96 1DIT 0 JRNL AUTH R.KRISHNAN,A.TULINSKY,G.P.VLASUK,D.PEARSON,P.VALLAR, JRNL AUTH 2 P.BERGUM,T.K.BRUNCK,W.C.RIPKA JRNL TITL SYNTHESIS, STRUCTURE, AND STRUCTURE-ACTIVITY RELATIONSHIPS JRNL TITL 2 OF DIVALENT THROMBIN INHIBITORS CONTAINING AN JRNL TITL 3 ALPHA-KETO-AMIDE TRANSITION-STATE MIMETIC. JRNL REF PROTEIN SCI. V. 5 422 1996 JRNL REFN ISSN 0961-8368 JRNL PMID 8868478 REMARK 1 REMARK 1 REFERENCE 1 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 1 REFERENCE 2 REMARK 1 AUTH E.SKRZYPCZAK-JANKUN,V.E.CARPEROS,K.G.RAVICHANDRAN, REMARK 1 AUTH 2 A.TULINSKY,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 3 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 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 3 NUMBER OF REFLECTIONS : 13022 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) : 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) : 0.1490 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 : 2365 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 165 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) : 0.020 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.035 ; 0.050 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.050 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.023 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.015 ; 0.020 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.220 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.280 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.250 ; 0.500 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) : 3.000 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 22.000; 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) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.100 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 A FEW SIDE CHAINS IN BOTH THROMBIN AND RECEPTOR PEPTIDE DO REMARK 3 NOT HAVE WELL-DEFINED ELECTRON DENSITY. THESE ATOMS HAVE REMARK 3 BEEN GIVEN OCCUPANCIES OF 0.01 IN THE ENTRY. IN ADDITION REMARK 3 RESIDUES ARG A 75, ARG A 126, AND GLN A 244 HAVE NO SIDE REMARK 3 CHAIN ATOMS AS THEY DO NOT HAVE ELECTRON DENSITY. REMARK 4 REMARK 4 1DIT 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_1000172807. 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 : 14238 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 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 (%): 51.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 35.45000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.10000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, P 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 *P* IS USED FOR THE DIVALENT INHIBITOR CVS995. 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 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 PRO P 17 REMARK 465 GLU P 18 REMARK 465 TYR P 19 REMARK 465 LEU P 20 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 ARG H 75 CG CD NE CZ NH1 NH2 REMARK 470 ARG H 126 CG CD NE CZ NH1 NH2 REMARK 470 GLN H 244 CG CD OE1 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 O ARG H 101 N ASP H 102 1.67 REMARK 500 NE ARG L 14D OE2 GLU L 14H 1.98 REMARK 500 O THR H 172 O HOH H 420 2.08 REMARK 500 NE2 GLN H 151 O GLY P 7 2.12 REMARK 500 O ARG H 101 N ILE H 103 2.12 REMARK 500 OG1 THR H 60I ND2 ASN H 62 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 LEU L 12 C GLU L 13 N -0.174 REMARK 500 ASN H 78 N ASN H 78 CA 0.139 REMARK 500 ARG H 93 CD ARG H 93 NE 0.102 REMARK 500 ARG H 101 C ASP H 102 N -0.496 REMARK 500 CYS H 191 C GLU H 192 N 0.279 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 GLY L 1D CA - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 GLY L 1D O - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 LYS L 9 CB - CG - CD ANGL. DEV. = 35.3 DEGREES REMARK 500 LYS L 10 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 LEU L 12 O - C - N ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG L 14D NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 SER H 20 O - C - N ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 SER H 27 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG H 35 NH1 - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG H 35 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -11.3 DEGREES REMARK 500 CYS H 42 N - CA - CB ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG H 50 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 TYR H 60A CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP H 63 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP H 63 CB - CG - OD2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG H 67 CG - CD - NE ANGL. DEV. = 28.2 DEGREES REMARK 500 ARG H 67 CD - NE - CZ ANGL. DEV. = 45.6 DEGREES REMARK 500 ARG H 67 NE - CZ - NH1 ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 THR H 74 N - CA - CB ANGL. DEV. = -12.0 DEGREES REMARK 500 GLU H 77 CA - C - O ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG H 77A CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG H 77A CA - C - O ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG H 77A CA - C - N ANGL. DEV. = 19.4 DEGREES REMARK 500 ASN H 78 C - N - CA ANGL. DEV. = -17.9 DEGREES REMARK 500 GLU H 80 CG - CD - OE1 ANGL. DEV. = -12.5 DEGREES REMARK 500 SER H 83 N - CA - CB ANGL. DEV. = 9.2 DEGREES REMARK 500 SER H 83 O - C - N ANGL. DEV. = 11.9 DEGREES REMARK 500 LEU H 85 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 LEU H 85 O - C - N ANGL. DEV. = 11.2 DEGREES REMARK 500 HIS H 91 CG - ND1 - CE1 ANGL. DEV. = 6.0 DEGREES REMARK 500 HIS H 91 CE1 - NE2 - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG H 93 CB - CG - CD ANGL. DEV. = 20.8 DEGREES REMARK 500 ARG H 93 CG - CD - NE ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG H 93 CD - NE - CZ ANGL. DEV. = -17.2 DEGREES REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG H 93 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG H 97 NH1 - CZ - NH2 ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -10.0 DEGREES REMARK 500 GLU H 97A OE1 - CD - OE2 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG H 101 CB - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG H 101 O - C - N ANGL. DEV. = -16.3 DEGREES REMARK 500 PHE H 114 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ASP H 116 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 76 ANGLE DEVIATIONS. 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 GLU L 1C 17.20 -156.30 REMARK 500 PHE L 7 -85.28 -132.75 REMARK 500 TYR L 14J 30.87 -70.85 REMARK 500 PRO H 37 170.94 -56.11 REMARK 500 ALA H 44 178.81 179.44 REMARK 500 SER H 48 -166.72 -170.79 REMARK 500 TYR H 60A 80.60 -151.04 REMARK 500 ASN H 60G 67.81 -153.40 REMARK 500 HIS H 71 -56.48 -136.17 REMARK 500 ASP H 102 77.40 -44.26 REMARK 500 ASN H 179 21.19 -78.44 REMARK 500 ASN H 205 23.64 49.37 REMARK 500 ASN P 10 27.36 49.21 REMARK 500 ASP P 12 37.48 -52.79 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 PRO P 3 0MG P 4 140.37 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 L 4 0.21 SIDE CHAIN REMARK 500 ARG H 50 0.30 SIDE CHAIN REMARK 500 ARG H 73 0.15 SIDE CHAIN REMARK 500 ARG H 93 0.32 SIDE CHAIN REMARK 500 ARG H 101 0.16 SIDE CHAIN REMARK 500 ARG H 221A 0.17 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 ARG H 101 11.65 REMARK 500 GLU H 192 14.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN P OF PEPTIDE INHIBITOR REMARK 800 CVS995 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 1DIT L 1H 14N UNP P00734 THRB_HUMAN 328 363 DBREF 1DIT H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1DIT P 1 20 PDB 1DIT 1DIT 1 20 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 P 20 2PP ASP PRO 0MG GLY GLY GLY GLY GLY ASN GLY ASP PHE SEQRES 2 P 20 GLU GLU ILE PRO GLU TYR LEU HET 2PP P 1 9 HET 0MG P 4 13 HETNAM 2PP 2-PROPYL-PENTANOIC ACID HETNAM 0MG AMINO{[(4S)-4-AMINO-5-CARBOXY-5- HETNAM 2 0MG OXOPENTYL]AMINO}METHANIMINIUM FORMUL 3 2PP C8 H16 O2 FORMUL 3 0MG C7 H15 N4 O3 1+ FORMUL 4 HOH *165(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 1.98 SSBOND 2 CYS H 42 CYS H 58 1555 1555 1.98 SSBOND 3 CYS H 168 CYS H 182 1555 1555 1.98 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK OG SER H 195 CA 0MG P 4 1555 1555 1.74 LINK C1 2PP P 1 N ASP P 2 1555 1555 1.33 LINK C PRO P 3 N 0MG P 4 1555 1555 1.35 LINK C 0MG P 4 N GLY P 5 1555 1555 1.41 CISPEP 1 SER H 36A PRO H 37 0 -4.37 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 SITE 1 AC1 32 PHE H 34 PRO H 37 GLN H 38 GLU H 39 SITE 2 AC1 32 LEU H 40 LEU H 41 HIS H 57 LYS H 60F SITE 3 AC1 32 LEU H 65 ARG H 73 THR H 74 ARG H 75 SITE 4 AC1 32 TYR H 76 GLN H 151 ASP H 189 ALA H 190 SITE 5 AC1 32 CYS H 191 GLY H 193 ASP H 194 SER H 195 SITE 6 AC1 32 SER H 214 TRP H 215 GLY H 216 GLU H 217 SITE 7 AC1 32 GLY H 219 GLY H 226 HOH H 424 HOH P 403 SITE 8 AC1 32 HOH P 423 HOH P 525 HOH P 639 HOH P 741 CRYST1 70.900 72.200 73.200 90.00 100.90 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 0.014104 0.000000 0.002716 0.00000 SCALE2 0.000000 0.013850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013912 0.00000