HEADER HYDROLASE/HYDROLASE INHIBITOR 22-JAN-01 1GHX TITLE A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED TITLE 2 SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN, RESIDUES 328-363; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN; COMPND 9 CHAIN: H; COMPND 10 FRAGMENT: HEAVY CHAIN, RESIDUES 364-620; COMPND 11 SYNONYM: COAGULATION FACTOR II; COMPND 12 EC: 3.4.21.5; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ACETYL HIRUDIN; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 12 ORGANISM_TAXID: 6421 KEYWDS THREE-CENTERED, VERY SHORT HYDROGEN BOND, OXYANION HOLE WATER, SHIFT KEYWDS 2 OF PKA OF HIS57, STRUCTURE-BASED DRUG DESIGN, SPECIFICITY, KEYWDS 3 UROKINASE, TRYPSIN, THROMBIN, ZN+2-MEDIATED INHIBITION, BLOOD KEYWDS 4 CLOTTING, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.KATZ,K.ELROD,C.LUONG,M.RICE,R.L.MACKMAN,P.A.SPRENGELER,J.SPENCER, AUTHOR 2 J.HATAYTE,J.JANC,J.LINK,J.LITVAK,R.RAI,K.RICE,S.SIDERIS,E.VERNER, AUTHOR 3 W.YOUNG REVDAT 7 25-DEC-24 1GHX 1 REMARK LINK REVDAT 6 27-DEC-23 1GHX 1 REMARK LINK REVDAT 5 04-OCT-17 1GHX 1 REMARK REVDAT 4 13-JUL-11 1GHX 1 VERSN REVDAT 3 24-FEB-09 1GHX 1 VERSN REVDAT 2 01-APR-03 1GHX 1 JRNL REVDAT 1 22-JAN-02 1GHX 0 JRNL AUTH B.A.KATZ,K.ELROD,C.LUONG,M.J.RICE,R.L.MACKMAN, JRNL AUTH 2 P.A.SPRENGELER,J.SPENCER,J.HATAYE,J.JANC,J.LINK,J.LITVAK, JRNL AUTH 3 R.RAI,K.RICE,S.SIDERIS,E.VERNER,W.YOUNG JRNL TITL A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A JRNL TITL 2 MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE JRNL TITL 3 SITE. JRNL REF J.MOL.BIOL. V. 307 1451 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11292354 JRNL DOI 10.1006/JMBI.2001.4516 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.800 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 65.7 REMARK 3 NUMBER OF REFLECTIONS : 29751 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) : 0.207 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2882 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 : 2417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 265 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.700 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: REMARK 3 GLU_H18, ASP_H21, MET_H84, AND VAL_H157 WERE SIMULTANEOUSLY REMARK 3 REFINED IN TWO CONFORMATIONS. REMARK 3 LYS_L9 IS ALSO DISORDERED. IN ONE CONFORMATION IT MAKES AN UNUSUAL REMARK 3 COORDINATE BOND TO ZN+2. REMARK 3 (ZN+2 HAD BEEN ADDED TO THE CRYSTAL IN THE HOPE OF BINDING AT THE REMARK 3 ACTIVE SITE. THE ZN+2 REMARK 3 COORDINATED BY LYS_L9 IS ON THE SURFACE AND THERE IS NO ZN+2 AT REMARK 3 THE ACTIVE SITE). REMARK 3 (RECENTLY DAN RICH AND COWORKERS FOUND THAT THE AMIDINE OF BABIM REMARK 3 CAN COORDINATE ZN+2) REMARK 3 NO DENSITY WAS OBSERVED FOR TRP148, THR149, ALA149A, ASN149B, REMARK 3 VAL149C, REMARK 3 GLY149D, AND LYS149E IN THE AUTOLYSIS LOOP, AND THESE RESIDUES ARE REMARK 3 NOT REMARK 3 INCLUDED IN THE MODEL. NO DENSITY WAS OBSERVED FOR C-TERMINAL REMARK 3 RESIDUES REMARK 3 OF THE HEAVY CHAIN FOLLOWING PHE_H245. RESIDUES AFTER PHE_H245 ARE REMARK 3 NOT REMARK 3 INCLUDED IN THE MODEL. REMARK 3 REMARK 3 HOH477 MAKES A SHORT HYDROGEN BOND WITH OGSER195 AND WITH O6' OF REMARK 3 THE INHIBITOR REMARK 3 REMARK 3 DISORDERED WATERS INCLUDE: REMARK 3 HOH394 WHICH IS IN A SPECIAL POSITION. (IT IS CLOSE REMARK 3 TO A SYMMETRY RELATED EQUIVALENT OF ITSELF); REMARK 3 HOH395 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH396 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH397 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF. REMARK 3 THE ABOVE "WATERS" CORRESPOND TO DENSITY THAT IS MORE ELECTRON REMARK 3 DENSE THAN WATERS. REMARK 3 THE OCCUPANCIES WERE ALLOWED TO REFINE TO VALUES GREATER THAN REMARK 3 UNITY. REMARK 3 HOH674 WHICH IS CLOSE TO HOH675; REMARK 3 HOH1127 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH1128; REMARK 3 REMARK 3 HIS_H57 IS DOUBLY PROTONATED. REMARK 3 HIS_H91 AND HIS_H119 ARE MONOPROTONATED ON THE EPSILON NITROGEN REMARK 4 REMARK 4 1GHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000001529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36570 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 42.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 27.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36400 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NACL (SOAK AT PH 8.2), PH REMARK 280 7.3, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH H 394 LIES ON A SPECIAL POSITION. 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 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G 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 O1 TYS I 63 H1 HOH I 735 1.12 REMARK 500 OG SER H 195 H2 HOH H 477 1.16 REMARK 500 HG SER H 195 O6' BMZ H 246 1.19 REMARK 500 H ASP H 222 H2 HOH H 809 1.24 REMARK 500 O ARG H 77A H1 HOH H 395 1.26 REMARK 500 O HOH H 536 H1 HOH H 624 1.33 REMARK 500 O HOH H 794 H2 HOH H 1226 1.39 REMARK 500 O HOH L 759 H1 HOH L 1020 1.47 REMARK 500 OG SER L 11 H2 HOH L 758 1.47 REMARK 500 H2 HOH I 953 O HOH I 1011 1.49 REMARK 500 O ASP H 170 H1 HOH H 525 1.50 REMARK 500 OG SER H 195 HN3 BMZ H 246 1.54 REMARK 500 O TRP H 96 H2 HOH H 466 1.55 REMARK 500 O6' BMZ H 246 H1 HOH H 477 1.55 REMARK 500 O VAL H 121 H2 HOH H 442 1.56 REMARK 500 OG1 THR H 74 H2 HOH H 489 1.57 REMARK 500 O TYR H 225 H2 HOH H 1210 1.57 REMARK 500 O ASN H 159 H1 HOH H 1321 1.57 REMARK 500 O LEU L 12 H2 HOH L 440 1.57 REMARK 500 O LYS H 110 H1 HOH H 897 1.58 REMARK 500 O ILE H 47 H1 HOH H 442 1.58 REMARK 500 O ASP L 14 H2 HOH L 739 1.59 REMARK 500 O TRP H 141 H2 HOH H 496 1.59 REMARK 500 O ASP H 243 H2 HOH H 1281 1.59 REMARK 500 O THR H 139 H1 HOH H 403 1.59 REMARK 500 O VAL H 163 H1 HOH H 418 1.60 REMARK 500 OH TYR H 208 H2 HOH H 862 1.60 REMARK 500 OG SER H 195 O6' BMZ H 246 2.01 REMARK 500 O1 TYS I 63 O HOH I 735 2.08 REMARK 500 OG SER H 195 O HOH H 477 2.08 REMARK 500 O ARG H 77A O HOH H 395 2.10 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 HOH H 396 O HOH H 396 2555 0.48 REMARK 500 O HOH H 395 O HOH H 395 2555 0.78 REMARK 500 H2 HOH H 396 H2 HOH H 396 2555 0.83 REMARK 500 H2 HOH H 395 H2 HOH H 395 2555 0.83 REMARK 500 O HOH H 396 H1 HOH H 396 2555 0.91 REMARK 500 O HOH H 396 H2 HOH H 396 2555 0.94 REMARK 500 O HOH H 395 H2 HOH H 395 2555 0.98 REMARK 500 H1 HOH H 396 H1 HOH H 396 2555 1.19 REMARK 500 H2 HOH H 397 O HOH H 444 2555 1.30 REMARK 500 O HOH H 499 H2 HOH H 1219 3445 1.57 REMARK 500 O HOH H 513 O HOH H 1047 2656 2.19 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 H 57 NE2 HIS H 57 CD2 -0.068 REMARK 500 HIS H 91 NE2 HIS H 91 CD2 -0.079 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY L 1F N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG H 73 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS H 122 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 TYR H 134 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 PHE H 199 N - CA - C ANGL. DEV. = -18.0 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 L 1G 177.92 -59.66 REMARK 500 SER L 1E -66.01 -135.85 REMARK 500 ALA L 1B -56.71 83.62 REMARK 500 PHE L 7 -97.73 -126.88 REMARK 500 ASP L 14L 103.38 88.80 REMARK 500 LEU H 41 -60.01 -99.44 REMARK 500 TYR H 60A 80.09 -159.72 REMARK 500 ASN H 60G 85.47 -158.99 REMARK 500 ASN H 62 2.87 -57.65 REMARK 500 HIS H 71 -56.97 -131.53 REMARK 500 ILE H 79 -50.10 -123.19 REMARK 500 GLU H 186B -33.77 -140.07 REMARK 500 ASP H 189 164.22 178.11 REMARK 500 LEU I 64 -66.07 -104.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG L 15 0.24 SIDE CHAIN REMARK 500 ARG H 50 0.21 SIDE CHAIN REMARK 500 ARG H 67 0.12 SIDE CHAIN REMARK 500 ARG H 93 0.15 SIDE CHAIN REMARK 500 ARG H 97 0.10 SIDE CHAIN REMARK 500 ARG H 101 0.12 SIDE CHAIN REMARK 500 ARG H 173 0.23 SIDE CHAIN REMARK 500 ARG H 187 0.14 SIDE CHAIN REMARK 500 ARG H 233 0.25 SIDE CHAIN 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 L 697 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH L 911 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH H 499 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH H 508 DISTANCE = 22.85 ANGSTROMS REMARK 525 HOH H 509 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH H 549 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH H 570 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH H 684 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH H 694 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH H 761 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH H 776 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH H 785 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH H 792 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH H 794 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH H 858 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH H 903 DISTANCE = 16.27 ANGSTROMS REMARK 525 HOH H 955 DISTANCE = 13.40 ANGSTROMS REMARK 525 HOH H1023 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH H1047 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH H1115 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH H1274 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH H1308 DISTANCE = 7.26 ANGSTROMS 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 ZN L 859 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 1A OD2 REMARK 620 2 LYS L 9 NZ 92.0 REMARK 620 3 HIS H 119 NE2 83.7 96.1 REMARK 620 4 HOH H 856 O 144.7 121.3 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA H 673 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 78.8 REMARK 620 3 PHE H 204A O 92.7 88.7 REMARK 620 4 HOH H 432 O 91.4 77.2 164.3 REMARK 620 5 HOH H 667 O 76.9 152.5 79.8 115.9 REMARK 620 6 HOH H1162 O 166.2 98.6 73.6 101.3 101.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 100.6 REMARK 620 3 HOH H 416 O 173.6 75.8 REMARK 620 4 HOH H 419 O 97.4 92.9 77.6 REMARK 620 5 HOH H 445 O 97.5 160.6 85.5 77.9 REMARK 620 6 HOH H 447 O 87.6 83.4 97.2 174.3 104.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 673 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 859 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMZ H 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF ACETYL HIRUDIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C5N RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT INHIBITOR DBREF 1GHX L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1GHX H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 1GHX I 55 65 UNP P28504 HIR2_HIRME 55 65 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 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 257 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 1GHX TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 24 HET ZN L 859 1 HET CA H 673 1 HET NA H 409 1 HET BMZ H 246 31 HETNAM TYS O-SULFO-L-TYROSINE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 ZN ZN 2+ FORMUL 5 CA CA 2+ FORMUL 6 NA NA 1+ FORMUL 7 BMZ C14 H13 N4 O 1+ FORMUL 8 HOH *265(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B TYR L 14J 1 9 HELIX 3 3 ALA H 55 CYS H 58 5 4 HELIX 4 4 PRO H 60B ASP H 60E 5 4 HELIX 5 5 THR H 60I ASN H 62 5 3 HELIX 6 6 ASP H 125 LEU H 130 1 9 HELIX 7 7 GLU H 164 THR H 172 1 9 HELIX 8 8 VAL H 231 PHE H 245 1 15 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 A 7 TRP H 207 GLY H 216 -1 N TYR H 208 O MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 N PHE H 227 O TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 O VAL H 66 N SER H 83 SHEET 3 B 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67 SHEET 4 B 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 5 B 7 TRP H 51 THR H 54 -1 N LEU H 53 O SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SSBOND 1 CYS L 1 CYS H 122 1555 1555 1.99 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.02 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.02 LINK C GLU I 62 N TYS I 63 1555 1555 1.31 LINK C TYS I 63 N LEU I 64 1555 1555 1.30 LINK OD2 ASP L 1A ZN ZN L 859 1555 1555 2.27 LINK NZ BLYS L 9 ZN ZN L 859 1555 1555 2.48 LINK ZN ZN L 859 NE2 HIS H 119 1555 1555 2.09 LINK ZN ZN L 859 O HOH H 856 1555 1555 2.75 LINK O LYS H 169 CA CA H 673 4556 1555 2.35 LINK O THR H 172 CA CA H 673 4556 1555 2.31 LINK O PHE H 204A CA CA H 673 1555 1555 2.35 LINK O ARG H 221A NA NA H 409 1555 1555 2.43 LINK O LYS H 224 NA NA H 409 1555 1555 2.41 LINK NA NA H 409 O HOH H 416 1555 1555 2.71 LINK NA NA H 409 O HOH H 419 1555 1555 2.70 LINK NA NA H 409 O HOH H 445 1555 1555 2.62 LINK NA NA H 409 O HOH H 447 1555 1555 2.63 LINK O HOH H 432 CA CA H 673 4556 1555 2.45 LINK O HOH H 667 CA CA H 673 1555 1555 2.39 LINK CA CA H 673 O HOH H1162 1555 1555 2.37 CISPEP 1 SER H 36A PRO H 37 0 -20.11 SITE 1 AC1 6 LYS H 169 THR H 172 PHE H 204A HOH H 432 SITE 2 AC1 6 HOH H 667 HOH H1162 SITE 1 AC2 4 HIS H 119 HOH H 856 ASP L 1A LYS L 9 SITE 1 AC3 6 ARG H 221A LYS H 224 HOH H 416 HOH H 419 SITE 2 AC3 6 HOH H 445 HOH H 447 SITE 1 AC4 11 HIS H 57 TRP H 60D ASP H 189 ALA H 190 SITE 2 AC4 11 GLU H 192 SER H 195 VAL H 213 GLY H 219 SITE 3 AC4 11 HOH H 477 HOH H 619 HOH H 620 SITE 1 AC5 19 PHE H 34 LYS H 36 GLN H 38 LEU H 65 SITE 2 AC5 19 ARG H 67 ARG H 73 THR H 74 ARG H 75 SITE 3 AC5 19 TYR H 76 GLU H 80 LYS H 81 ILE H 82 SITE 4 AC5 19 MET H 84 HOH H 471 HOH H1248 HOH I 520 SITE 5 AC5 19 HOH I 535 HOH I 666 HOH I 735 CRYST1 72.300 71.950 72.960 90.00 101.54 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013831 0.000000 0.002824 0.00000 SCALE2 0.000000 0.013899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013989 0.00000