HEADER HYDROLASE/HYDROLASE INHIBITOR 10-DEC-99 1DLK TITLE CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL TITLE 2 CHLOROMETHYL KETONE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RESIDUES 1-13; COMPND 5 EC: 3.4.21.1; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: B, D; COMPND 9 FRAGMENT: RESIDUES 16-245; COMPND 10 EC: 3.4.21.1; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PEPTIDIC INHIBITOR; COMPND 13 CHAIN: E, F; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: PANCREAS; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 8 ORGANISM_COMMON: CATTLE; SOURCE 9 ORGANISM_TAXID: 9913; SOURCE 10 ORGAN: PANCREAS; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHETICALLY CONSTRUCTED KEYWDS DELTA-CHYMOTRYPSIN, PEPTIDIC INHIBIOR, CHLOROMETHYL KETONE, KEYWDS 2 HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MAC SWEENEY,G.BIRRANE,M.A.WALSH,T.O'CONNELL,J.P.G.MALTHOUSE REVDAT 5 12-SEP-18 1DLK 1 REMARK REVDAT 4 13-JUL-11 1DLK 1 VERSN REVDAT 3 24-FEB-09 1DLK 1 VERSN REVDAT 2 01-APR-03 1DLK 1 JRNL REVDAT 1 03-MAY-00 1DLK 0 JRNL AUTH A.MAC SWEENEY,G.BIRRANE,M.A.WALSH,T.O'CONNELL,J.P.MALTHOUSE, JRNL AUTH 2 T.M.HIGGINS JRNL TITL CRYSTAL STRUCTURE OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL JRNL TITL 2 CHLOROMETHYL KETONE INHIBITOR. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 280 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10713514 JRNL DOI 10.1107/S0907444999016583 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.5 REMARK 3 NUMBER OF REFLECTIONS : 45515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2428 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.20 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.018 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.000 ; 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: USED MAXIMUM LIKELIHOOD PROCEDURE REMARK 4 REMARK 4 1DLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39978 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6 M AMMONIUM SULFATE, 200 MM MES REMARK 280 -HCL, 10 MM COCL2, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 58.04000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.58500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.58500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.02000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.58500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.58500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.06000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.58500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.58500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.02000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.58500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.58500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 87.06000 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 58.04000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 APPLY THE FOLLOWING TO CHAINS: C, D, F REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 181.75500 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -60.58500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 29.02000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 3 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: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F 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 THE PEPTIDIC INHIBITOR BINDS TO THROMBIN THROUGH TWO COVALENT BONDS: REMARK 400 A BOND BETWEEN 0QE AND HIS 57 AND A HEMIKETAL BETWEEN HPH AND SER REMARK 400 195. REMARK 400 REMARK 400 THE Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) IS PEPTIDE-LIKE, REMARK 400 A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) REMARK 400 CHAIN: E REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: The chlorormethyl ketone inhibitor linked to the REMARK 400 protein through two covalent bonds with the active REMARK 400 site serine and histidine REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 SER C 11 REMARK 475 GLY C 12 REMARK 475 LEU C 13 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 7 CB CG CD OE1 NE2 REMARK 480 LEU A 13 C O CB CG CD1 CD2 REMARK 480 LYS B 36 CG CD CE NZ REMARK 480 LYS B 79 CD CE NZ REMARK 480 LYS B 82 NZ REMARK 480 LYS B 84 CD CE NZ REMARK 480 LYS B 87 CD CE NZ REMARK 480 LYS B 93 NZ REMARK 480 LYS B 170 CE NZ REMARK 480 LYS D 36 CE NZ REMARK 480 LYS D 79 CE NZ REMARK 480 ARG D 145 NE CZ NH1 NH2 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 CL CL B 400 O HOH B 504 1.73 REMARK 500 O HOH D 401 O HOH D 403 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 VAL C 3 O HOH B 456 8665 1.20 REMARK 500 SD MET B 192 O HOH D 356 3645 1.77 REMARK 500 CE MET B 192 N GLY F 2 3645 1.95 REMARK 500 C VAL C 3 O HOH B 456 8665 1.98 REMARK 500 N PRO C 4 O HOH B 456 8665 2.03 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 A 13 CA LEU A 13 CB 0.289 REMARK 500 LYS B 36 CB LYS B 36 CG -0.205 REMARK 500 LYS B 87 CG LYS B 87 CD -0.210 REMARK 500 MET B 192 CB MET B 192 CG 0.235 REMARK 500 MET B 192 SD MET B 192 CE 1.173 REMARK 500 VAL C 3 C VAL C 3 O 0.218 REMARK 500 LYS D 79 CD LYS D 79 CE -0.174 REMARK 500 ARG D 145 CD ARG D 145 NE -0.153 REMARK 500 GLY E 2 N GLY E 2 CA 0.186 REMARK 500 GLY E 2 CA GLY E 2 C 0.160 REMARK 500 GLY F 2 N GLY F 2 CA 0.170 REMARK 500 GLY F 2 CA GLY F 2 C 0.136 REMARK 500 GLY F 2 C GLY F 2 O 0.124 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 PRO B 24 N - CA - CB ANGL. DEV. = 8.1 DEGREES REMARK 500 LYS B 36 CA - CB - CG ANGL. DEV. = 19.8 DEGREES REMARK 500 LYS B 87 CB - CG - CD ANGL. DEV. = 19.0 DEGREES REMARK 500 ASN B 91 CA - CB - CG ANGL. DEV. = 23.8 DEGREES REMARK 500 LYS B 93 CD - CE - NZ ANGL. DEV. = -23.9 DEGREES REMARK 500 MET B 192 CA - CB - CG ANGL. DEV. = -15.2 DEGREES REMARK 500 MET B 192 CA - CB - CG ANGL. DEV. = -15.8 DEGREES REMARK 500 MET B 192 CG - SD - CE ANGL. DEV. = -22.8 DEGREES REMARK 500 MET B 192 CA - C - O ANGL. DEV. = -15.4 DEGREES REMARK 500 THR B 219 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 VAL B 235 CA - CB - CG2 ANGL. DEV. = 13.9 DEGREES REMARK 500 VAL C 3 C - N - CA ANGL. DEV. = -16.4 DEGREES REMARK 500 VAL C 3 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 VAL C 3 N - CA - C ANGL. DEV. = -24.3 DEGREES REMARK 500 VAL C 3 CA - C - O ANGL. DEV. = -30.5 DEGREES REMARK 500 VAL C 3 CA - C - N ANGL. DEV. = 28.4 DEGREES REMARK 500 VAL C 3 O - C - N ANGL. DEV. = -20.6 DEGREES REMARK 500 PRO C 4 C - N - CA ANGL. DEV. = 22.6 DEGREES REMARK 500 PRO C 4 C - N - CD ANGL. DEV. = -30.7 DEGREES REMARK 500 LEU C 10 CA - C - O ANGL. DEV. = -13.2 DEGREES REMARK 500 PRO D 28 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP D 35 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 PHE D 71 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ASP D 72 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 LYS D 82 CD - CE - NZ ANGL. DEV. = 14.9 DEGREES REMARK 500 SER D 113 N - CA - CB ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP D 128 CB - CG - OD1 ANGL. DEV. = 14.1 DEGREES REMARK 500 ASP D 153 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG D 154 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU D 163 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 ASP D 178 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 SER D 195 CB - CA - C ANGL. DEV. = -13.8 DEGREES REMARK 500 THR D 208 CA - CB - OG1 ANGL. DEV. = -13.0 DEGREES REMARK 500 THR D 208 CA - CB - CG2 ANGL. DEV. = 18.4 DEGREES REMARK 500 THR D 219 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 THR D 219 CA - CB - CG2 ANGL. DEV. = 11.1 DEGREES REMARK 500 VAL D 235 CG1 - CB - CG2 ANGL. DEV. = 17.3 DEGREES REMARK 500 GLY E 2 CA - C - N ANGL. DEV. = 28.8 DEGREES REMARK 500 GLY E 2 O - C - N ANGL. DEV. = -20.9 DEGREES REMARK 500 GLY E 3 C - N - CA ANGL. DEV. = 14.2 DEGREES REMARK 500 GLY E 3 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 GLY F 2 CA - C - N ANGL. DEV. = 24.9 DEGREES REMARK 500 GLY F 2 O - C - N ANGL. DEV. = -18.7 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 PHE B 71 -54.73 -124.79 REMARK 500 SER B 115 -164.19 -161.74 REMARK 500 SER B 186 23.65 -142.24 REMARK 500 SER B 214 -65.02 -123.63 REMARK 500 ASN D 48 -175.42 -175.17 REMARK 500 PHE D 71 -57.20 -120.31 REMARK 500 SER D 214 -66.73 -128.67 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 VAL C 3 PRO C 4 136.59 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 ASN B 91 -10.53 REMARK 500 VAL C 3 -58.67 REMARK 500 GLY E 3 20.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF PEPTIDIC INHIBITOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF PEPTIDIC INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GCH RELATED DB: PDB REMARK 900 REFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS REMARK 900 RESOLUTION DBREF 1DLK A 1 13 UNP P00766 CTRA_BOVIN 1 13 DBREF 1DLK B 16 245 UNP P00766 CTRA_BOVIN 16 245 DBREF 1DLK C 1 13 UNP P00766 CTRA_BOVIN 1 13 DBREF 1DLK D 16 245 UNP P00766 CTRA_BOVIN 16 245 DBREF 1DLK E 1 5 PDB 1DLK 1DLK 1 5 DBREF 1DLK F 1 5 PDB 1DLK 1DLK 1 5 SEQRES 1 A 13 CYS GLY VAL PRO ALA ILE GLN PRO VAL LEU SER GLY LEU SEQRES 1 B 230 ILE VAL ASN GLY GLU GLU ALA VAL PRO GLY SER TRP PRO SEQRES 2 B 230 TRP GLN VAL SER LEU GLN ASP LYS THR GLY PHE HIS PHE SEQRES 3 B 230 CYS GLY GLY SER LEU ILE ASN GLU ASN TRP VAL VAL THR SEQRES 4 B 230 ALA ALA HIS CYS GLY VAL THR THR SER ASP VAL VAL VAL SEQRES 5 B 230 ALA GLY GLU PHE ASP GLN GLY SER SER SER GLU LYS ILE SEQRES 6 B 230 GLN LYS LEU LYS ILE ALA LYS VAL PHE LYS ASN SER LYS SEQRES 7 B 230 TYR ASN SER LEU THR ILE ASN ASN ASP ILE THR LEU LEU SEQRES 8 B 230 LYS LEU SER THR ALA ALA SER PHE SER GLN THR VAL SER SEQRES 9 B 230 ALA VAL CYS LEU PRO SER ALA SER ASP ASP PHE ALA ALA SEQRES 10 B 230 GLY THR THR CYS VAL THR THR GLY TRP GLY LEU THR ARG SEQRES 11 B 230 TYR THR ASN ALA ASN THR PRO ASP ARG LEU GLN GLN ALA SEQRES 12 B 230 SER LEU PRO LEU LEU SER ASN THR ASN CYS LYS LYS TYR SEQRES 13 B 230 TRP GLY THR LYS ILE LYS ASP ALA MET ILE CYS ALA GLY SEQRES 14 B 230 ALA SER GLY VAL SER SER CYS MET GLY ASP SER GLY GLY SEQRES 15 B 230 PRO LEU VAL CYS LYS LYS ASN GLY ALA TRP THR LEU VAL SEQRES 16 B 230 GLY ILE VAL SER TRP GLY SER SER THR CYS SER THR SER SEQRES 17 B 230 THR PRO GLY VAL TYR ALA ARG VAL THR ALA LEU VAL ASN SEQRES 18 B 230 TRP VAL GLN GLN THR LEU ALA ALA ASN SEQRES 1 C 13 CYS GLY VAL PRO ALA ILE GLN PRO VAL LEU SER GLY LEU SEQRES 1 D 230 ILE VAL ASN GLY GLU GLU ALA VAL PRO GLY SER TRP PRO SEQRES 2 D 230 TRP GLN VAL SER LEU GLN ASP LYS THR GLY PHE HIS PHE SEQRES 3 D 230 CYS GLY GLY SER LEU ILE ASN GLU ASN TRP VAL VAL THR SEQRES 4 D 230 ALA ALA HIS CYS GLY VAL THR THR SER ASP VAL VAL VAL SEQRES 5 D 230 ALA GLY GLU PHE ASP GLN GLY SER SER SER GLU LYS ILE SEQRES 6 D 230 GLN LYS LEU LYS ILE ALA LYS VAL PHE LYS ASN SER LYS SEQRES 7 D 230 TYR ASN SER LEU THR ILE ASN ASN ASP ILE THR LEU LEU SEQRES 8 D 230 LYS LEU SER THR ALA ALA SER PHE SER GLN THR VAL SER SEQRES 9 D 230 ALA VAL CYS LEU PRO SER ALA SER ASP ASP PHE ALA ALA SEQRES 10 D 230 GLY THR THR CYS VAL THR THR GLY TRP GLY LEU THR ARG SEQRES 11 D 230 TYR THR ASN ALA ASN THR PRO ASP ARG LEU GLN GLN ALA SEQRES 12 D 230 SER LEU PRO LEU LEU SER ASN THR ASN CYS LYS LYS TYR SEQRES 13 D 230 TRP GLY THR LYS ILE LYS ASP ALA MET ILE CYS ALA GLY SEQRES 14 D 230 ALA SER GLY VAL SER SER CYS MET GLY ASP SER GLY GLY SEQRES 15 D 230 PRO LEU VAL CYS LYS LYS ASN GLY ALA TRP THR LEU VAL SEQRES 16 D 230 GLY ILE VAL SER TRP GLY SER SER THR CYS SER THR SER SEQRES 17 D 230 THR PRO GLY VAL TYR ALA ARG VAL THR ALA LEU VAL ASN SEQRES 18 D 230 TRP VAL GLN GLN THR LEU ALA ALA ASN SEQRES 1 E 5 PHQ GLY GLY HPH 0QE SEQRES 1 F 5 PHQ GLY GLY HPH 0QE HET PHQ E 1 10 HET HPH E 4 11 HET 0QE E 5 1 HET PHQ F 1 10 HET HPH F 4 11 HET 0QE F 5 1 HET CL B 400 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM HPH (2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL HETNAM 0QE CHLOROMETHANE HETNAM CL CHLORIDE ION HETSYN HPH (2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL HETSYN 0QE CHLORO METHYL GROUP FORMUL 5 PHQ 2(C8 H7 CL O2) FORMUL 5 HPH 2(C9 H13 N O2) FORMUL 5 0QE 2(C H3 CL) FORMUL 7 CL CL 1- FORMUL 8 HOH *281(H2 O) HELIX 1 1 ALA B 55 GLY B 59 5 5 HELIX 2 2 SER B 164 GLY B 173 1 10 HELIX 3 3 THR B 174 ILE B 176 5 3 HELIX 4 4 VAL B 231 ASN B 245 1 15 HELIX 5 5 ALA D 55 GLY D 59 5 5 HELIX 6 6 SER D 164 GLY D 173 1 10 HELIX 7 7 THR D 174 ILE D 176 5 3 HELIX 8 8 LEU D 234 ALA D 244 1 11 SHEET 1 A 8 GLU B 20 GLU B 21 0 SHEET 2 A 8 GLN B 156 LEU B 163 -1 N GLN B 157 O GLU B 20 SHEET 3 A 8 THR B 135 GLY B 140 -1 N CYS B 136 O LEU B 160 SHEET 4 A 8 PRO B 198 LYS B 203 -1 O PRO B 198 N THR B 139 SHEET 5 A 8 ALA B 206 TRP B 215 -1 O ALA B 206 N LYS B 203 SHEET 6 A 8 PRO B 225 ARG B 230 -1 N VAL B 227 O TRP B 215 SHEET 7 A 8 MET B 180 GLY B 184 -1 N ILE B 181 O TYR B 228 SHEET 8 A 8 GLN B 156 LEU B 163 -1 O PRO B 161 N GLY B 184 SHEET 1 B 7 GLN B 30 GLN B 34 0 SHEET 2 B 7 HIS B 40 LEU B 46 -1 N PHE B 41 O LEU B 33 SHEET 3 B 7 TRP B 51 THR B 54 -1 N VAL B 53 O SER B 45 SHEET 4 B 7 THR B 104 LEU B 108 -1 O THR B 104 N THR B 54 SHEET 5 B 7 GLN B 81 LYS B 90 -1 N ALA B 86 O LYS B 107 SHEET 6 B 7 VAL B 65 ALA B 68 -1 N VAL B 66 O LEU B 83 SHEET 7 B 7 GLN B 30 GLN B 34 -1 O SER B 32 N VAL B 67 SHEET 1 C 7 GLU D 20 GLU D 21 0 SHEET 2 C 7 GLN D 156 PRO D 161 -1 O GLN D 157 N GLU D 20 SHEET 3 C 7 THR D 135 GLY D 140 -1 N CYS D 136 O LEU D 160 SHEET 4 C 7 PRO D 198 LYS D 203 -1 O PRO D 198 N THR D 139 SHEET 5 C 7 ALA D 206 TRP D 215 -1 O ALA D 206 N LYS D 203 SHEET 6 C 7 PRO D 225 ARG D 230 -1 N VAL D 227 O TRP D 215 SHEET 7 C 7 MET D 180 GLY D 184 -1 N ILE D 181 O TYR D 228 SHEET 1 D 7 GLN D 30 GLN D 34 0 SHEET 2 D 7 HIS D 40 ASN D 48 -1 N PHE D 41 O LEU D 33 SHEET 3 D 7 TRP D 51 THR D 54 -1 O TRP D 51 N ILE D 47 SHEET 4 D 7 THR D 104 LEU D 108 -1 O THR D 104 N THR D 54 SHEET 5 D 7 GLN D 81 LYS D 90 -1 N ALA D 86 O LYS D 107 SHEET 6 D 7 VAL D 65 ALA D 68 -1 O VAL D 66 N LEU D 83 SHEET 7 D 7 GLN D 30 GLN D 34 -1 O SER D 32 N VAL D 67 SSBOND 1 CYS A 1 CYS B 122 1555 1555 1.97 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.01 SSBOND 3 CYS B 136 CYS B 201 1555 1555 1.99 SSBOND 4 CYS B 168 CYS B 182 1555 1555 2.06 SSBOND 5 CYS B 191 CYS B 220 1555 1555 1.97 SSBOND 6 CYS C 1 CYS D 122 1555 1555 1.94 SSBOND 7 CYS D 42 CYS D 58 1555 1555 2.07 SSBOND 8 CYS D 136 CYS D 201 1555 1555 1.96 SSBOND 9 CYS D 168 CYS D 182 1555 1555 1.94 SSBOND 10 CYS D 191 CYS D 220 1555 1555 1.97 LINK OG SER D 195 C HPH F 4 1555 1555 1.53 LINK OG SER B 195 C HPH E 4 1555 1555 1.58 LINK NE2 HIS B 57 C1 0QE E 5 1555 1555 1.59 LINK NE2 HIS D 57 C1 0QE F 5 1555 1555 1.62 LINK C1 PHQ E 1 N GLY E 2 1555 1555 1.38 LINK C1 PHQ F 1 N GLY F 2 1555 1555 1.38 LINK C GLY E 3 N HPH E 4 1555 1555 1.43 LINK C HPH E 4 C1 0QE E 5 1555 1555 1.62 LINK C GLY F 3 N HPH F 4 1555 1555 1.39 LINK C HPH F 4 C1 0QE F 5 1555 1555 1.64 SITE 1 AC1 3 LYS B 90 HOH B 504 GLY D 59 SITE 1 AC2 16 HIS B 57 LEU B 97 THR B 98 LYS B 175 SITE 2 AC2 16 SER B 190 MET B 192 GLY B 193 SER B 195 SITE 3 AC2 16 SER B 214 TRP B 215 GLY B 216 SER B 217 SITE 4 AC2 16 HOH B 453 SER D 218 HOH E 441 HOH F 294 SITE 1 AC3 19 MET B 192 SER B 218 HIS D 57 LEU D 97 SITE 2 AC3 19 THR D 98 LYS D 175 SER D 190 GLY D 193 SITE 3 AC3 19 SER D 195 SER D 214 TRP D 215 GLY D 216 SITE 4 AC3 19 SER D 217 HOH D 275 HOH D 290 HOH D 386 SITE 5 AC3 19 HOH E 441 HOH F 294 HOH F 383 CRYST1 121.170 121.170 116.080 90.00 90.00 90.00 P 41 21 2 16 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 0.008253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008615 0.00000 MTRIX1 1 0.036840 -0.491830 0.869910 0.56850 1 MTRIX2 1 0.997910 -0.028060 -0.058120 -0.14946 1 MTRIX3 1 0.052990 0.870240 0.489770 -0.35459 1