HEADER HYDROLASE/HYDROLASE INHIBITOR 28-APR-93 2HPP TITLE STRUCTURES OF THE NONCOVALENT COMPLEXES OF HUMAN AND BOVINE TITLE 2 PROTHROMBIN FRAGMENT 2 WITH HUMAN PPACK-THROMBIN CAVEAT 2HPP INTERACTIONS INVOLVING LYS H 236 ARE OUTSIDE ACCEPTED RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: UNP RESIDUES 328-363; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ALPHA-THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 FRAGMENT: UNP RESIDUES 364-622; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PROTHROMBIN; COMPND 13 CHAIN: P; COMPND 14 FRAGMENT: UNP RESIDUES 214-292; COMPND 15 SYNONYM: COAGULATION FACTOR II; COMPND 16 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 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 11 ORGANISM_COMMON: BOVINE; SOURCE 12 ORGANISM_TAXID: 9913 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX, SERINE PROTEINASE EXPDTA X-RAY DIFFRACTION AUTHOR A.TULINSKY,K.PADMANABHAN REVDAT 4 13-JUL-11 2HPP 1 VERSN REVDAT 3 24-FEB-09 2HPP 1 VERSN REVDAT 2 01-APR-03 2HPP 1 JRNL REVDAT 1 31-JAN-94 2HPP 0 JRNL AUTH R.K.ARNI,K.PADMANABHAN,K.P.PADMANABHAN,T.P.WU,A.TULINSKY JRNL TITL STRUCTURES OF THE NONCOVALENT COMPLEXES OF HUMAN AND BOVINE JRNL TITL 2 PROTHROMBIN FRAGMENT 2 WITH HUMAN PPACK-THROMBIN. JRNL REF BIOCHEMISTRY V. 32 4727 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8387813 JRNL DOI 10.1021/BI00069A006 REMARK 1 REMARK 1 REFERENCE 1 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 2 REMARK 1 AUTH T.-P.WU,K.PADMANABHAN,A.TULINSKY,A.M.MULICHAK REMARK 1 TITL THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID REMARK 1 TITL 2 COMPLEX OF HUMAN PLASMINOGEN KRINGLE 4 REMARK 1 REF BIOCHEMISTRY V. 30 10589 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.P.SESHADRI,A.TULINSKY,E.SKRZYPCZAK-JANKUN,C.H.PARK REMARK 1 TITL STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 220 481 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL 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) : 0.157 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 : 2882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 119 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) : 0.012 ; NULL REMARK 3 ANGLE DISTANCE (A) : 3.400 ; 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 A FEW SIDE CHAINS IN BOTH THROMBIN AND FRAGMENT 2 DO NOT REMARK 3 HAVE WELL DEFINED ELECTRON DENSITY. THESE ATOMS HAVE BEEN REMARK 3 GIVEN OCCUPANCIES OF 0.0 IN THE FILE FOR THE FOLLOWING: REMARK 3 ARG 310, ARG 312, THR 316, ARG 321, SER 327, REMARK 3 GLU 328, VAL 343, AND ASN 377. IN ADDITION THERE WAS NO REMARK 3 ELECTRON DENSITY FOR THE 14 N-TERMINAL AND 25 C-TERMINAL REMARK 3 INTERKRINGLE PEPTIDES. REMARK 4 REMARK 4 2HPP 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 (%): 72.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 51.85000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 61.35000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.92500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.35000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 61.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.77500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.92500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 61.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.77500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.85000 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, 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 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 14M REMARK 465 ARG L 14N REMARK 465 THR H 148A REMARK 465 ALA H 148B REMARK 465 ASN H 148C REMARK 465 VAL H 148D REMARK 465 GLY H 148E REMARK 465 LYS H 148F REMARK 465 GLY H 246 REMARK 465 GLU H 247 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 TRP H 148 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 470 TRP H 148 CZ2 CZ3 CH2 REMARK 470 PHE H 245 CB CG CD1 CD2 CE1 CE2 CZ 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 NZ LYS H 236 OD1 ASP P 338 1.08 REMARK 500 CE LYS H 236 OD1 ASP P 338 1.19 REMARK 500 NZ LYS H 240 O LYS P 335 1.45 REMARK 500 CD GLU L 1C O HOH H 454 1.68 REMARK 500 NZ LYS H 236 CG ASP P 338 1.73 REMARK 500 O ASP P 304 N GLY P 306 1.89 REMARK 500 CG GLU L 1C O HOH H 454 1.89 REMARK 500 CD LYS H 236 OD1 ASP P 338 1.91 REMARK 500 OE1 GLU L 1C O HOH H 454 2.04 REMARK 500 O THR H 60I N ASN H 62 2.07 REMARK 500 O LYS H 224 O HOH H 402 2.09 REMARK 500 NH2 ARG H 187 OD1 ASP H 222 2.10 REMARK 500 OD2 ASP P 356 OH TYR P 373 2.10 REMARK 500 OD2 ASP L 14 NH2 ARG H 137 2.13 REMARK 500 NZ LYS H 236 OD2 ASP P 338 2.15 REMARK 500 OG1 THR P 316 OE1 GLU P 372 2.16 REMARK 500 NH1 ARG P 305 O GLU P 358 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 GLY P 359 C ALA P 360 N 0.224 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG L 14D NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG L 14D NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LEU L 14G O - C - N ANGL. DEV. = 11.8 DEGREES REMARK 500 SER H 20 N - CA - CB ANGL. DEV. = -9.0 DEGREES REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ASP H 21 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU H 33 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 PHE H 34 C - N - CA ANGL. DEV. = 17.6 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU H 41 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LEU H 65 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG H 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG H 73 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR H 76 N - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG H 77A O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 HIS H 91 CA - CB - CG ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG H 93 NE - CZ - NH2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG H 97 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG H 101 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP H 116 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP H 116 O - C - N ANGL. DEV. = 9.7 DEGREES REMARK 500 LEU H 123 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG H 137 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASN H 143 O - C - N ANGL. DEV. = 10.9 DEGREES REMARK 500 SER H 153 N - CA - CB ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG H 165 CD - NE - CZ ANGL. DEV. = 11.3 DEGREES REMARK 500 CYS H 168 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP H 170 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG H 175 CD - NE - CZ ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG H 175 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 CYS H 182 CA - C - O ANGL. DEV. = -12.8 DEGREES REMARK 500 CYS H 182 O - C - N ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 LYS H 186D N - CA - CB ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG H 187 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP H 194 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP H 194 CB - CG - OD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG H 206 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLN H 209 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 GLN H 209 O - C - N ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG H 233 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG H 233 NH1 - CZ - NH2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG H 233 NE - CZ - NH2 ANGL. DEV. = 8.3 DEGREES REMARK 500 GLN H 239 N - CA - CB ANGL. DEV. = 12.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 ALA L 1B -26.75 -167.95 REMARK 500 PHE L 7 -89.56 -133.39 REMARK 500 SER L 11 46.77 71.39 REMARK 500 LYS L 14A -9.78 -48.06 REMARK 500 THR L 14B -4.87 -147.06 REMARK 500 GLU H 18 37.62 73.74 REMARK 500 SER H 36A 127.33 -178.63 REMARK 500 ALA H 44 -179.30 -175.65 REMARK 500 HIS H 57 -13.21 -48.88 REMARK 500 TYR H 60A 83.86 -166.51 REMARK 500 GLU H 61 21.29 -51.00 REMARK 500 HIS H 71 -55.87 -126.77 REMARK 500 THR H 74 -77.64 -92.97 REMARK 500 ILE H 79 -66.74 -101.13 REMARK 500 GLU H 97A -92.93 -130.55 REMARK 500 ARG H 101 42.65 72.78 REMARK 500 ASN H 179 37.93 -95.54 REMARK 500 GLU H 186B 3.10 -69.02 REMARK 500 ASN H 204B -9.14 -143.36 REMARK 500 VAL H 213 106.85 -52.54 REMARK 500 SER H 214 -67.89 -92.16 REMARK 500 TRP H 215 -150.72 -159.06 REMARK 500 GLN H 244 -74.35 -78.68 REMARK 500 PRO P 303 -101.29 -61.13 REMARK 500 ARG P 305 50.92 -25.42 REMARK 500 ARG P 307 -8.34 -53.52 REMARK 500 GLU P 308 22.93 -157.84 REMARK 500 ARG P 310 71.29 -115.59 REMARK 500 ALA P 314 22.93 -160.80 REMARK 500 ALA P 324 115.64 -26.28 REMARK 500 TRP P 325 -33.57 -37.33 REMARK 500 SER P 327 176.81 -47.63 REMARK 500 ALA P 332 -72.73 -68.11 REMARK 500 ALA P 342 -57.60 -157.19 REMARK 500 VAL P 343 98.76 -64.37 REMARK 500 GLU P 347 -97.42 40.94 REMARK 500 ASN P 348 31.32 -143.30 REMARK 500 ASP P 354 -72.22 -78.75 REMARK 500 ASP P 356 117.66 -30.49 REMARK 500 VAL P 364 -6.25 -143.75 REMARK 500 ALA P 365 -165.38 -174.26 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 97 0.20 SIDE CHAIN REMARK 500 ARG P 310 0.23 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 L 14D 24.3 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 411 DISTANCE = 5.50 ANGSTROMS REMARK 525 HOH H 413 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH H 428 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH H 450 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH H 465 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH H 481 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH H 482 DISTANCE = 5.40 ANGSTROMS REMARK 525 HOH H 499 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH H 523 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH H 543 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH H 561 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH H 563 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH H 580 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH H 581 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH H 615 DISTANCE = 11.12 ANGSTROMS REMARK 525 HOH H 630 DISTANCE = 8.67 ANGSTROMS REMARK 525 HOH H 633 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH L 410 DISTANCE = 5.43 ANGSTROMS REMARK 525 HOH L 544 DISTANCE = 5.43 ANGSTROMS REMARK 525 HOH L 560 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH L 575 DISTANCE = 9.52 ANGSTROMS REMARK 525 HOH L 579 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH P 423 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH P 426 DISTANCE = 13.16 ANGSTROMS REMARK 525 HOH P 427 DISTANCE = 9.72 ANGSTROMS REMARK 525 HOH P 436 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH P 459 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH P 547 DISTANCE = 9.91 ANGSTROMS REMARK 525 HOH P 568 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH P 582 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH P 598 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH P 628 DISTANCE = 10.78 ANGSTROMS REMARK 525 HOH P 636 DISTANCE = 5.64 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG- REMARK 600 CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN THE INHIBITOR REMARK 600 COVALENTLY BINDS TO THE ACTIVE SITE RESIDUE NE2 HIS H 57 VIA A REMARK 600 METHYLENE GROUP REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO- REMARK 630 2-OXOHEXAN-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 0G7 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO ARG 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 0G7 H 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HPQ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSIN NUMBERING SYSTEM IS USED, BASED ON THE TOPOLOGICAL REMARK 999 ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, REMARK 999 EMBO J. 8, 3467-3475). THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND REMARK 999 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN REMARK 999 INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *P* IS REMARK 999 USED FOR PROTHROMBIN FRAGMENT 2. DBREF 2HPP L 1H 14N UNP P00734 THRB_HUMAN 328 363 DBREF 2HPP H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 2HPP P 301 379 UNP P00735 THRB_BOVIN 214 292 SEQADV 2HPP ASN P 375 UNP P00735 ASP 288 CONFLICT 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 79 CYS VAL PRO ASP ARG GLY ARG GLU TYR ARG GLY ARG LEU SEQRES 2 P 79 ALA VAL THR THR SER GLY SER ARG CYS LEU ALA TRP SER SEQRES 3 P 79 SER GLU GLN ALA LYS ALA LEU SER LYS ASP GLN ASP PHE SEQRES 4 P 79 ASN PRO ALA VAL PRO LEU ALA GLU ASN PHE CYS ARG ASN SEQRES 5 P 79 PRO ASP GLY ASP GLU GLU GLY ALA TRP CYS TYR VAL ALA SEQRES 6 P 79 ASP GLN PRO GLY ASP PHE GLU TYR CYS ASN LEU ASN TYR SEQRES 7 P 79 CYS HET 0G7 H 1 30 HETNAM 0G7 D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2- HETNAM 2 0G7 OXOHEXAN-3-YL]-L-PROLINAMIDE HETSYN 0G7 D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) FORMUL 4 0G7 C21 H31 CL N6 O3 FORMUL 5 HOH *119(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 HELIX 5 K5 GLU P 328 LYS P 335 1DISTORTED TWO-TURN HELIX 8 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 SHEET 1 B3 2 ALA P 314 THR P 316 0 SHEET 2 B3 2 SER P 320 CYS P 322 -1 SHEET 1 B4 2 ALA P 360 TYR P 363 0 SHEET 2 B4 2 PHE P 371 CYS P 374 -1 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.03 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 SSBOND 5 CYS P 301 CYS P 379 1555 1555 2.06 SSBOND 6 CYS P 322 CYS P 362 1555 1555 2.52 SSBOND 7 CYS P 350 CYS P 374 1555 1555 2.10 LINK NE2 HIS H 57 C3 0G7 H 1 1555 1555 1.71 CISPEP 1 SER H 36A PRO H 37 0 -1.29 SITE 1 AC1 14 HIS H 57 TYR H 60A GLU H 97A LEU H 99 SITE 2 AC1 14 ILE H 174 ASP H 189 ALA H 190 CYS H 191 SITE 3 AC1 14 GLY H 193 SER H 195 SER H 214 TRP H 215 SITE 4 AC1 14 GLY H 216 GLY H 219 CRYST1 122.700 122.700 103.700 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008150 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009643 0.00000