3HK6 - Header Asymmetric Unit

HEADER HYDROLASE 22-MAY-09 3HK6

TITLE CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A (TWO TITLE 2 MOLECULES IN THE ASYMMETRIC UNIT)

COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: LIGHT CHAIN: UNP RESIDUES 317-360; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: HEAVY CHAIN: UNP RESIDUES 361-618; COMPND 12 SYNONYM: COAGULATION FACTOR II; COMPND 13 EC: 3.4.21.5; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: F2, CF2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_ORGAN: BABY HAMSTER KIDNEY; SOURCE 9 EXPRESSION_SYSTEM_CELL: BHK CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: HPC4-PNUT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: F2, CF2; SOURCE 16 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 18 EXPRESSION_SYSTEM_ORGAN: BABY HAMSTER KIDNEY; SOURCE 19 EXPRESSION_SYSTEM_CELL: BHK CELLS; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: HPC4-PNUT

KEYWDS SERINE PROTEASE, ACUTE PHASE, BLOOD COAGULATION, CALCIUM, KEYWDS 2 CLEAVAGE ON PAIR OF BASIC RESIDUES, DISULFIDE BOND, GAMMA- KEYWDS 3 CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, HYDROLASE, KRINGLE, KEYWDS 4 PROTEASE, ZYMOGEN

EXPDTA X-RAY DIFFRACTION

AUTHOR P.S.GANDHI,M.J.PAGE,Z.CHEN,L.BUSH-PELC,E.DI CERA

REVDAT 2 15-SEP-09 3HK6 1 JRNL REVDAT 1 07-JUL-09 3HK6 0

JRNL AUTH P.S.GANDHI,M.J.PAGE,Z.CHEN,L.BUSH-PELC,E.DI CERA JRNL TITL MECHANISM OF THE ANTICOAGULANT ACTIVITY OF THROMBIN JRNL TITL 2 MUTANT W215A/E217A. JRNL REF J.BIOL.CHEM. V. 284 24098 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19586901 JRNL DOI 10.1074/JBC.M109.025403

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.O.PINEDA,Z.W.CHEN,S.CACCIA,A.M.CANTWELL, REMARK 1 AUTH 2 S.N.SAVVIDES,G.WAKSMAN,F.S.MATHEWS,E.DI CERA REMARK 1 TITL THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A REMARK 1 TITL 2 COLLAPSED PRIMARY SPECIFICITY POCKET. REMARK 1 REF J.BIOL.CHEM. V. 279 39824 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15252033 REMARK 1 DOI 10.1074/JBC.M407272200

REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 11572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 583 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 630 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.19000 REMARK 3 B22 (A**2) : 2.19000 REMARK 3 B33 (A**2) : -4.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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): 0.679 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.489 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.591 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.900 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.803 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5010 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6776 ; 1.926 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 596 ; 8.203 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 234 ;35.669 ;23.077 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 884 ;23.287 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;16.515 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 718 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3796 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2992 ; 0.680 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4840 ; 1.304 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2018 ; 1.720 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1936 ; 2.981 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 3HK6 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09. REMARK 100 THE RCSB ID CODE IS RCSB053233.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12201 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1TQ0 REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM AMMONIUM DIHYDROGEN REMARK 280 PHOSPHATE, 14% PEG 3350, PH 4.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K

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 146.54000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.19700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.19700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.27000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.19700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.19700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 219.81000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.19700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.19700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.27000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.19700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.19700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 219.81000 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 146.54000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY CONSISTS OF A AND B CHAINS.

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ARG A 15 REMARK 465 ARG C 15

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 HIS A 1O CG ND1 CD2 CE1 NE2 REMARK 470 HIS C 1O CG ND1 CD2 CE1 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 NH2 ARG D 165 O MET D 180 2.08 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 CYS B 42 CB CYS B 42 SG -0.115 REMARK 500 CYS D 42 CB CYS D 42 SG -0.114 REMARK 500 ALA D 215 C GLY D 216 N 0.140 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 GLU B 149E N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 LYS B 222 CD - CE - NZ ANGL. DEV. = 19.0 DEGREES REMARK 500 VAL D 90 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG D 175 NE - CZ - NH1 ANGL. DEV. = 3.4 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 THR A 1N 164.14 -43.84 REMARK 500 PHE A 1M -91.47 -115.82 REMARK 500 GLU A 1J -42.31 -26.88 REMARK 500 PHE A 7 -76.02 -123.39 REMARK 500 LYS A 9 3.68 -67.38 REMARK 500 LYS A 10 11.43 -143.18 REMARK 500 SER A 11 -36.05 69.42 REMARK 500 LEU A 12 132.87 -33.49 REMARK 500 THR A 14A -32.17 -28.86 REMARK 500 ASP A 14H 3.91 -58.08 REMARK 500 ASP A 14L -151.02 -69.71 REMARK 500 GLU B 18 43.75 32.95 REMARK 500 PRO B 37 -164.48 -67.14 REMARK 500 CYS B 42 158.29 178.92 REMARK 500 ALA B 44 121.45 -174.67 REMARK 500 ASP B 49 28.94 -61.26 REMARK 500 ARG B 50 -23.72 -161.54 REMARK 500 ASP B 60E 59.36 70.69 REMARK 500 ASN B 60G 41.53 -147.18 REMARK 500 HIS B 71 -79.74 -124.14 REMARK 500 SER B 72 108.25 -49.45 REMARK 500 ARG B 73 -25.88 -39.54 REMARK 500 THR B 74 -30.36 -139.84 REMARK 500 ARG B 75 106.02 -39.83 REMARK 500 TYR B 76 92.00 -63.46 REMARK 500 VAL B 79 -67.48 -151.07 REMARK 500 GLU B 97A -82.59 -77.58 REMARK 500 ASP B 116 -7.95 -58.79 REMARK 500 HIS B 119 124.61 -172.37 REMARK 500 VAL B 129 -52.60 -27.72 REMARK 500 ALA B 132 119.07 -39.21 REMARK 500 GLU B 146 125.35 -17.73 REMARK 500 THR B 149A -149.96 24.77 REMARK 500 ASN B 149D -36.96 123.72 REMARK 500 ILE B 150 8.82 55.62 REMARK 500 PRO B 152 153.06 -39.97 REMARK 500 ASP B 178 -35.50 -24.36 REMARK 500 LYS B 186D -154.77 -92.00 REMARK 500 ARG B 187 -13.80 -155.01 REMARK 500 VAL B 213 109.88 -52.83 REMARK 500 ALA B 215 88.13 -166.98 REMARK 500 CYS B 220 -100.49 79.55 REMARK 500 LYS B 222 22.32 13.16 REMARK 500 LYS C 1I -51.94 -29.95 REMARK 500 PHE C 7 -67.81 -139.46 REMARK 500 LYS C 10 9.32 -65.50 REMARK 500 ILE C 14K -112.86 -73.65 REMARK 500 VAL D 17 108.35 -51.35 REMARK 500 TRP D 20 148.93 179.06 REMARK 500 SER D 36A 107.56 -171.79 REMARK 500 GLN D 38 70.71 -63.59 REMARK 500 CYS D 42 166.89 179.82 REMARK 500 ALA D 44 167.33 179.37 REMARK 500 ASP D 49 -5.26 -48.69 REMARK 500 HIS D 71 -73.89 -105.56 REMARK 500 THR D 74 -65.48 -121.37 REMARK 500 TYR D 76 96.48 -66.68 REMARK 500 ASN D 78 -22.84 83.36 REMARK 500 VAL D 79 -64.04 -105.17 REMARK 500 TYR D 94 109.19 -40.61 REMARK 500 ASN D 98 173.49 155.32 REMARK 500 ARG D 101 44.56 70.32 REMARK 500 ASP D 102 87.88 -69.65 REMARK 500 SER D 115 -154.61 169.69 REMARK 500 HIS D 119 120.70 -171.20 REMARK 500 TRP D 148 5.43 84.27 REMARK 500 THR D 149A -153.50 40.22 REMARK 500 ASN D 149D -49.80 139.17 REMARK 500 ILE D 150 -57.28 64.08 REMARK 500 VAL D 186 -49.51 -5.08 REMARK 500 ASN D 186A -61.36 -122.94 REMARK 500 ASP D 186B 126.92 16.65 REMARK 500 THR D 186C 25.20 -58.52 REMARK 500 PHE D 204A -97.50 -117.53 REMARK 500 ASN D 204B -5.65 -58.61 REMARK 500 SER D 214 -61.12 -98.25 REMARK 500 CYS D 220 -121.00 58.96 REMARK 500 LYS D 222 15.53 48.49 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 ASN B 149D GLU B 149E 149.27 REMARK 500 ASN D 149D GLU D 149E 149.81 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, 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 GLY B 219 10.10 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 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: (11X,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 GLU A 14C 24.0 L L OUTSIDE RANGE REMARK 500 THR B 74 23.7 L L OUTSIDE RANGE REMARK 500 THR B 147 18.7 L L OUTSIDE RANGE REMARK 500 LYS B 222 23.2 L L OUTSIDE RANGE REMARK 500 ILE D 150 23.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TQ0 RELATED DB: PDB REMARK 900 THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A REMARK 900 COLLAPSED PRIMARY SPECIFICITY POCKET REMARK 900 RELATED ID: 3HK3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A REMARK 900 (ONE MOLECULE IN THE ASYMMETRIC UNIT) REMARK 900 RELATED ID: 3HKI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A IN REMARK 900 COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1 REMARK 900 RELATED ID: 3HKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT W215A/E217A IN REMARK 900 COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1

DBREF 3HK6 A 1P 15 UNP P19221 THRB_MOUSE 317 360 DBREF 3HK6 B 16 246 UNP P19221 THRB_MOUSE 361 618 DBREF 3HK6 C 1P 15 UNP P19221 THRB_MOUSE 317 360 DBREF 3HK6 D 16 246 UNP P19221 THRB_MOUSE 361 618

SEQADV 3HK6 ALA B 215 UNP P19221 TRP 587 ENGINEERED SEQADV 3HK6 ALA B 217 UNP P19221 GLU 589 ENGINEERED SEQADV 3HK6 ALA D 215 UNP P19221 TRP 587 ENGINEERED SEQADV 3HK6 ALA D 217 UNP P19221 GLU 589 ENGINEERED

SEQRES 1 A 44 PHE HIS THR PHE PHE ASN GLU LYS THR PHE GLY LEU GLY SEQRES 2 A 44 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 3 A 44 SER LEU LYS ASP THR THR GLU LYS GLU LEU LEU ASP SER SEQRES 4 A 44 TYR ILE ASP GLY ARG SEQRES 1 B 258 ILE VAL GLU GLY TRP ASP ALA GLU LYS GLY ILE ALA PRO SEQRES 2 B 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 258 THR ALA ALA HIS CYS ILE LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 258 HIS SER ARG THR ARG TYR GLU ARG ASN VAL GLU LYS ILE SEQRES 7 B 258 SER MET LEU GLU LYS ILE TYR VAL HIS PRO ARG TYR ASN SEQRES 8 B 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 B 258 LEU LYS LYS PRO VAL PRO PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 258 VAL CYS LEU PRO ASP LYS GLN THR VAL THR SER LEU LEU SEQRES 11 B 258 ARG ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 258 LEU ARG GLU THR TRP THR THR ASN ILE ASN GLU ILE GLN SEQRES 13 B 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 258 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 B 258 ASP ASN MET PHE CYS ALA GLY PHE LYS VAL ASN ASP THR SEQRES 16 B 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 258 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG LYS SEQRES 19 B 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 258 ARG TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 C 44 PHE HIS THR PHE PHE ASN GLU LYS THR PHE GLY LEU GLY SEQRES 2 C 44 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 3 C 44 SER LEU LYS ASP THR THR GLU LYS GLU LEU LEU ASP SER SEQRES 4 C 44 TYR ILE ASP GLY ARG SEQRES 1 D 258 ILE VAL GLU GLY TRP ASP ALA GLU LYS GLY ILE ALA PRO SEQRES 2 D 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 D 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 D 258 THR ALA ALA HIS CYS ILE LEU TYR PRO PRO TRP ASP LYS SEQRES 5 D 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 D 258 HIS SER ARG THR ARG TYR GLU ARG ASN VAL GLU LYS ILE SEQRES 7 D 258 SER MET LEU GLU LYS ILE TYR VAL HIS PRO ARG TYR ASN SEQRES 8 D 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 D 258 LEU LYS LYS PRO VAL PRO PHE SER ASP TYR ILE HIS PRO SEQRES 10 D 258 VAL CYS LEU PRO ASP LYS GLN THR VAL THR SER LEU LEU SEQRES 11 D 258 ARG ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 D 258 LEU ARG GLU THR TRP THR THR ASN ILE ASN GLU ILE GLN SEQRES 13 D 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 D 258 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 D 258 ASP ASN MET PHE CYS ALA GLY PHE LYS VAL ASN ASP THR SEQRES 16 D 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 D 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 D 258 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG LYS SEQRES 19 D 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 D 258 ARG TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY

HELIX 1 1 ASN A 1K GLY A 1F 1 6 HELIX 2 2 GLY A 1D CYS A 1 5 5 HELIX 3 3 PHE A 7 SER A 11 5 5 HELIX 4 4 THR A 14B ASP A 14H 1 7 HELIX 5 5 TYR B 60A ASP B 60E 5 5 HELIX 6 6 THR B 60I ASN B 62 5 3 HELIX 7 7 ASP B 125 LEU B 130 1 9 HELIX 8 8 GLU B 164 SER B 171 1 8 HELIX 9 9 CYS B 191 SER B 195 5 5 HELIX 10 10 LEU B 234 GLY B 246 1 13 HELIX 11 11 ASN C 1K GLY C 1F 1 6 HELIX 12 12 THR C 14B SER C 14I 1 8 HELIX 13 13 ALA D 55 CYS D 58 5 4 HELIX 14 14 PRO D 60B ASP D 60E 5 4 HELIX 15 15 THR D 60I ASN D 62 5 3 HELIX 16 16 ASP D 125 LEU D 130 1 9 HELIX 17 17 GLU D 164 THR D 172 1 9 HELIX 18 18 GLY D 219 LYS D 222 5 5 HELIX 19 19 LEU D 234 GLY D 246 1 13

SHEET 1 A 7 TRP B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N TRP B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N GLY B 140 O GLN B 156 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 ALA B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O THR B 229 N ILE B 212 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 LEU B 40 SER B 48 -1 O CYS B 42 N LEU B 33 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O LEU B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 VAL B 90 -1 N TYR B 89 O LEU B 105 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N MET B 32 O ARG B 67 SHEET 1 C 7 GLN D 30 ARG D 35 0 SHEET 2 C 7 LEU D 40 SER D 48 -1 O ALA D 44 N VAL D 31 SHEET 3 C 7 TRP D 51 THR D 54 -1 O LEU D 53 N SER D 45 SHEET 4 C 7 ALA D 104 LEU D 108 -1 O LEU D 106 N VAL D 52 SHEET 5 C 7 LYS D 81 VAL D 90 -1 N TYR D 89 O LEU D 105 SHEET 6 C 7 LEU D 64 ILE D 68 -1 N VAL D 66 O SER D 83 SHEET 7 C 7 GLN D 30 ARG D 35 -1 N MET D 32 O ARG D 67 SHEET 1 D 2 LEU D 60 TYR D 60A 0 SHEET 2 D 2 LYS D 60F ASN D 60G-1 O LYS D 60F N TYR D 60A SHEET 1 E 6 GLN D 156 PRO D 161 0 SHEET 2 E 6 LYS D 135 GLY D 140 -1 N VAL D 138 O VAL D 158 SHEET 3 E 6 PRO D 198 LYS D 202 -1 O VAL D 200 N ARG D 137 SHEET 4 E 6 TRP D 207 ALA D 215 -1 O TYR D 208 N MET D 201 SHEET 5 E 6 GLY D 226 HIS D 230 -1 O PHE D 227 N ALA D 215 SHEET 6 E 6 MET D 180 ALA D 183 -1 N PHE D 181 O TYR D 228

SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.02 SSBOND 2 CYS B 42 CYS B 58 1555 1555 1.98 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.06 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 5 CYS C 1 CYS D 122 1555 1555 2.00 SSBOND 6 CYS D 42 CYS D 58 1555 1555 2.01 SSBOND 7 CYS D 168 CYS D 182 1555 1555 2.00 SSBOND 8 CYS D 191 CYS D 220 1555 1555 2.03

CISPEP 1 SER B 36A PRO B 37 0 -10.51 CISPEP 2 SER D 36A PRO D 37 0 12.52

CRYST1 70.394 70.394 293.080 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 0.014206 0.000000 0.000000 0.00000

SCALE2 0.000000 0.014206 0.000000 0.00000

SCALE3 0.000000 0.000000 0.003412 0.00000