PDB Short entry for 1PPC HEADER HYDROLASE/HYDROLASE INHIBITOR 24-OCT-91 1PPC TITLE GEOMETRY OF BINDING OF THE BENZAMIDINE-AND ARGININE-BASED INHIBITORS TITLE 2 N-ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P-AMIDINOPHENYLALANYL- TITLE 3 PIPERIDINE (NAPAP) AND (2R,4R)-4-METHYL-1-[N-ALPHA-(3-METHYL-1,2,3,4- TITLE 4 TETRAHYDRO-8-QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC TITLE 5 ACID (MQPA) TO HUMAN ALPHA-THROMBIN: X-RAY CRYSTALLOGRAPHIC TITLE 6 DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF NAPAP- TITLE 7 THROMBIN AND MQPA-THROMBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: E; COMPND 4 EC: 3.4.21.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: COW; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.BODE,D.TURK REVDAT 5 13-JUL-11 1PPC 1 VERSN REVDAT 4 25-AUG-09 1PPC 1 SOURCE REVDAT 3 24-FEB-09 1PPC 1 VERSN REVDAT 2 01-APR-03 1PPC 1 JRNL REVDAT 1 31-JAN-94 1PPC 0 JRNL AUTH W.BODE,D.TURK,J.STURZEBECHER JRNL TITL GEOMETRY OF BINDING OF THE BENZAMIDINE- AND ARGININE-BASED JRNL TITL 2 INHIBITORS N JRNL TITL 3 ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P- JRNL TITL 4 AMIDINOPHENYLALANYL-PIPE RIDINE (NAPAP) AND JRNL TITL 5 (2R,4R)-4-METHYL-1-[N ALPHA-(3-METHYL-1,2,3,4-TETRAHYDR JRNL TITL 6 QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC ACID JRNL TITL 7 (MQPA) TO HUMAN ALPHA-THROMBIN.X-RAY CRYSTALLOGRAPHIC JRNL TITL 8 DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF JRNL TITL 9 NAPAP-THROMBIN AND MQPA-THROMBIN. JRNL REF EUR.J.BIOCHEM. V. 193 175 1990 JRNL REFN ISSN 0014-2956 JRNL PMID 2226434 JRNL DOI 10.1111/J.1432-1033.1990.TB19320.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.BRANDSTETTER,D.TURK,H.W.HOEFFKEN,D.GROSSE,J.STUERZEBECHER, REMARK 1 AUTH 2 P.D.MARTIN,B.F.EDWARDS,W.BODE REMARK 1 TITL REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE REMARK 1 TITL 2 THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND REMARK 1 TITL 3 ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA. REMARK 1 TITL 4 A STARTING POINT FOR IMPROVING ANTITHROMBOTICS REMARK 1 REF J.MOL.BIOL. V. 226 1085 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.BODE,D.TURK,A.KARSHIKOV REMARK 1 TITL THE REFINED 1.9 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF REMARK 1 TITL 2 D-PHE-PRO-ARG-CHLOROMETHYLKETONE-INHIBITED HUMAN REMARK 1 TITL 3 ALPHA-THROMBIN: STRUCTURE ANALYSIS, OVERALL STRUCTURE, REMARK 1 TITL 4 ELECTROSTATIC PROPERTIES, DETAILED ACTIVE-SITE GEOMETRY, AND REMARK 1 TITL 5 STRUCTURE-FUNCTION RELATIONSHIPS REMARK 1 REF PROTEIN SCI. V. 1 426 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.TURK,J.STUERZEBECHER,W.BODE REMARK 1 TITL GEOMETRY OF BINDING OF THE NALPHA-TOSYLATED PIPERIDIDES OF REMARK 1 TITL 2 M-AMIDINO-, P-AMIDINO-AND P-GUANIDINO PHENYLALANINE TO REMARK 1 TITL 3 THROMBIN AND TRYPSIN: X-RAY CRYSTAL STRUCTURES OF THEIR REMARK 1 TITL 4 TRYPSIN COMPLEXES AND MODELING OF THEIR THROMBIN COMPLEXES REMARK 1 REF FEBS LETT. V. 287 133 1991 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 4 REMARK 1 AUTH W.BODE,I.MAYR,U.BAUMANN,R.HUBER,S.R.STONE,J.HOFSTEENGE REMARK 1 TITL THE REFINED 1.9 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 1 REFERENCE 5 REMARK 1 AUTH H.D.BARTUNIK,L.J.SUMMERS,H.H.BARTSCH REMARK 1 TITL CRYSTAL STRUCTURE OF BOVINE BETA-TRYPSIN AT 1.5 ANGSTROMS REMARK 1 TITL 2 RESOLUTION IN A CRYSTAL FORM WITH LOW MOLECULAR PACKING REMARK 1 TITL 3 DENSITY. ACTIVE SITE GEOMETRY, ION PAIRS AND SOLVENT REMARK 1 TITL 4 STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 210 813 1989 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 6 REMARK 1 AUTH W.BODE,P.SCHWAGER REMARK 1 TITL THE REFINED CRYSTAL STRUCTURE OF BOVINE BETA-TRYPSIN AT 1.8 REMARK 1 TITL 2 ANGSTROMS RESOLUTION. CRYSTALLOGRAPHIC REFINEMENT, CALCIUM REMARK 1 TITL 3 BINDING SITE, BENZAMIDINE BINDING SITE AND ACTIVE SITE AT PH REMARK 1 TITL 4 7.0 REMARK 1 REF J.MOL.BIOL. V. 98 693 1975 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 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 SET) : 0.181 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1629 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 147 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 2.54 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PPC 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 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 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 31.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.90500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.90500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.59500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH E 814 O HOH E 863 2554 0.79 REMARK 500 O HOH E 911 O HOH E 968 2554 0.81 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 HIS E 57 NE2 HIS E 57 CD2 -0.071 REMARK 500 HIS E 91 NE2 HIS E 91 CD2 -0.077 REMARK 500 GLU E 186 CD GLU E 186 OE2 0.067 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TRP E 51 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP E 51 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG E 66 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG E 66 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU E 67 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG E 117 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 TRP E 141 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP E 141 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP E 215 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP E 215 CE2 - CD2 - CG ANGL. DEV. = -5.1 DEGREES REMARK 500 TRP E 237 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP E 237 CE2 - CD2 - CG ANGL. DEV. = -5.7 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 E 71 -82.36 -129.99 REMARK 500 ASN E 79 -6.82 81.95 REMARK 500 ASN E 115 -156.11 -169.31 REMARK 500 SER E 195 134.44 -35.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 NAPAP, A SYNTHETIC THROMBIN INHIBITOR, IS NONCOVALENTLY REMARK 600 BOUND TO THE ACTIVE SITE. A CALCIUM ION IS BOUND IN THE REMARK 600 "CALCIUM BINDING LOOP" (BODE AND SCHWAGER, 1975A,B). REMARK 600 REMARK 600 NAPAP [N==ALPHA==-(2-NAPHTHYL-SULFONYL-GLYCYL)-DL-P- REMARK 600 AMIDINOPHENYLALANYL-PIPERIDINE] "RESIDUES" ARE REMARK 600 IN REMARK 630 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 CA E 480 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU E 70 OE1 REMARK 620 2 ASN E 72 O 88.9 REMARK 620 3 VAL E 75 O 161.7 87.0 REMARK 620 4 GLU E 80 OE2 103.0 157.1 87.2 REMARK 620 5 HOH E 714 O 88.4 85.9 109.0 75.1 REMARK 620 6 HOH E 810 O 79.4 108.4 85.0 93.0 160.8 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4- REMARK 630 CARBAMIMIDOYL-D-PHENYLALANYL]PIPERIDINE 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 MID E 5 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NAS GLY APH PIP REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: NULL DBREF 1PPC E 16 245 UNP P00760 TRY1_BOVIN 21 243 SEQRES 1 E 223 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 E 223 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 E 223 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 E 223 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 E 223 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 E 223 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 E 223 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 E 223 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 E 223 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 E 223 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 E 223 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 E 223 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 E 223 THR SER ASN MET PHE CYS ALA GLY TYR LEU GLU GLY GLY SEQRES 14 E 223 LYS ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL SEQRES 15 E 223 CYS SER GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER SEQRES 16 E 223 GLY CYS ALA GLN LYS ASN LYS PRO GLY VAL TYR THR LYS SEQRES 17 E 223 VAL CYS ASN TYR VAL SER TRP ILE LYS GLN THR ILE ALA SEQRES 18 E 223 SER ASN HET MID E 5 37 HET CA E 480 1 HETNAM MID 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4-CARBAMIMIDOYL-D- HETNAM 2 MID PHENYLALANYL]PIPERIDINE HETNAM CA CALCIUM ION HETSYN MID NAPAP FORMUL 2 MID C27 H31 N5 O4 S FORMUL 3 CA CA 2+ FORMUL 4 HOH *147(H2 O) HELIX 1 1 ALA E 55 TYR E 59 5 5 HELIX 2 2 SER E 164 TYR E 172 1 9 HELIX 3 3 TYR E 234 SER E 244 1 11 SHEET 1 A 7 TYR E 20 THR E 21 0 SHEET 2 A 7 LYS E 156 PRO E 161 -1 N CYS E 157 O TYR E 20 SHEET 3 A 7 GLN E 135 GLY E 140 -1 N CYS E 136 O ALA E 160 SHEET 4 A 7 PRO E 198 CYS E 201 -1 O PRO E 198 N SER E 139 SHEET 5 A 7 LYS E 204 TRP E 215 -1 O LYS E 204 N CYS E 201 SHEET 6 A 7 GLY E 226 LYS E 230 -1 N VAL E 227 O TRP E 215 SHEET 7 A 7 MET E 180 ALA E 183 -1 O PHE E 181 N TYR E 228 SHEET 1 B 7 GLN E 30 ASN E 34 0 SHEET 2 B 7 HIS E 40 ASN E 48 -1 N PHE E 41 O LEU E 33 SHEET 3 B 7 TRP E 51 SER E 54 -1 O TRP E 51 N ILE E 47 SHEET 4 B 7 MET E 104 LEU E 108 -1 O MET E 104 N SER E 54 SHEET 5 B 7 GLN E 81 VAL E 90 -1 N SER E 86 O LYS E 107 SHEET 6 B 7 GLN E 64 LEU E 67 -1 N VAL E 65 O ILE E 83 SHEET 7 B 7 GLN E 30 ASN E 34 -1 O SER E 32 N ARG E 66 SSBOND 1 CYS E 22 CYS E 157 1555 1555 2.06 SSBOND 2 CYS E 42 CYS E 58 1555 1555 2.05 SSBOND 3 CYS E 128 CYS E 232 1555 1555 2.03 SSBOND 4 CYS E 136 CYS E 201 1555 1555 2.01 SSBOND 5 CYS E 168 CYS E 182 1555 1555 2.00 SSBOND 6 CYS E 191 CYS E 220 1555 1555 2.01 LINK OE1 GLU E 70 CA CA E 480 1555 1555 2.40 LINK O ASN E 72 CA CA E 480 1555 1555 2.32 LINK O VAL E 75 CA CA E 480 1555 1555 2.34 LINK OE2 GLU E 80 CA CA E 480 1555 1555 2.58 LINK CA CA E 480 O HOH E 714 1555 1555 2.41 LINK CA CA E 480 O HOH E 810 1555 1555 2.43 SITE 1 AC1 15 HIS E 57 ASN E 97 LEU E 99 ASP E 189 SITE 2 AC1 15 SER E 190 SER E 195 SER E 214 TRP E 215 SITE 3 AC1 15 GLY E 216 SER E 217 GLY E 219 GLY E 226 SITE 4 AC1 15 HOH E 416 HOH E 843 HOH E 948 SITE 1 AC2 6 GLU E 70 ASN E 72 VAL E 75 GLU E 80 SITE 2 AC2 6 HOH E 714 HOH E 810 CRYST1 63.510 69.190 63.810 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 0.015746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015672 0.00000