PDB Short entry for 1GI8 HEADER BLOOD CLOTTING, HYDROLASE 22-JAN-01 1GI8 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: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SHORT CHAIN; COMPND 5 SYNONYM: UPA, U-PLASMINOGEN ACTIVATOR, UROKINASE-PLASMINOGEN COMPND 6 ACTIVATOR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: CATALYTIC DOMAIN; COMPND 12 SYNONYM: UPA, U-PLASMINOGEN ACTIVATOR, UROKINASE-PLASMINOGEN COMPND 13 ACTIVATOR; COMPND 14 EC: 3.4.21.73; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPIC9LMWUPA; SOURCE 9 OTHER_DETAILS: CHEM.BIOL. 7, 299-312, 2000; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PPIC9LMWUPA; SOURCE 18 OTHER_DETAILS: CHEM.BIOL. 7, 299-312, 2000 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 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 5 27-DEC-23 1GI8 1 REMARK SEQADV LINK REVDAT 4 04-OCT-17 1GI8 1 REMARK REVDAT 3 24-FEB-09 1GI8 1 VERSN REVDAT 2 01-APR-03 1GI8 1 JRNL REVDAT 1 22-JAN-02 1GI8 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 67.8 REMARK 3 NUMBER OF REFLECTIONS : 16463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1616 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 : 2003 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 395 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) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 4.300 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 ONLY LEU_A9 TO THR_A17 ARE INCLUDED FOR THE A-CHAIN. REMARK 3 RESIDUES PRIOR AND AFTER THESE RESIDUES ARE NOT VISIBLE REMARK 3 (DISORDERED). REMARK 3 RESIDUES AFTER THR_B242 ARE NOT VISIBLE (DISORDERED). REMARK 3 REMARK 3 RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: REMARK 3 ILE_B17, THR_B22, MET_B47, ASP_B97, THR_B139, ARG_B166. REMARK 3 REMARK 3 DISORDERED WATERS ARE: REMARK 3 REMARK 3 HOH11 WHICH IS CLOSE TO HOH12; REMARK 3 HOH90 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH373 WHICH IS CLOSE TO HOH374; REMARK 3 HOH497 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH681 WHICH IS CLOSE TO HOH682; REMARK 3 HOH940 WHICH IS CLOSE TO HOH941, WHICH IN TURN IS CLOSE TO HOH942; REMARK 3 HOH980 WHICH IS CLOSE TO HOH981; REMARK 3 HOH1013 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH1017 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH1031 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 REMARK 3 NO ENERGY TERMS BETWEEN CITRATE 1 AND 2 ARE INCLUDED BECAUSE THEY REMARK 3 ARE REMARK 3 HYDROGEN-BONDED TO ONE ANOTHER VIA AN UNUSUALLY SHORT HYDROGEN BOND REMARK 3 BETWEEN CARBOXYLATE / HYDROXYL GROUPS. REMARK 3 REMARK 3 NO ENERGY TERMS ARE INCLUDED AMONG HOH_591, AND OGSER195, AND O6' REMARK 3 OF THE REMARK 3 INHIBITOR. THESE ATOMS FORM A VERY SHORT MULTI-CENTERED HYDROGEN- REMARK 3 BONDING NETWORK. REMARK 4 REMARK 4 1GI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000001540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.50 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 : 20030 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 40.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 44.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS 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 (%): 39.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL PEG 4000, PH 6.5, VAPOR REMARK 280 DIFFUSION AT 298 K, PH 6.50 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 41.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.38500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 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 B 314 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 447 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 LYS A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 PRO A 5 REMARK 465 PRO A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 8 REMARK 465 LEU A 18 REMARK 465 ARG A 19 REMARK 465 PRO A 20 REMARK 465 ARG A 21 REMARK 465 PHE A 22 REMARK 465 LYS A 23 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 HG SER B 195 O6' BMZ B 246 1.19 REMARK 500 HG SER B 195 H1 HOH B 477 1.24 REMARK 500 HZ1 LYS B 92 HE1 TRP B 237 1.31 REMARK 500 OG SER B 195 H1 HOH B 477 1.38 REMARK 500 O6' BMZ B 246 H2 HOH B 477 1.48 REMARK 500 OG1 THR B 177 H1 HOH B 261 1.50 REMARK 500 O GLY B 19 H1 HOH B 573 1.53 REMARK 500 O TYR B 64 H1 HOH B 499 1.54 REMARK 500 O TYR B 151 H2 HOH B 472 1.56 REMARK 500 O ALA B 183 H1 HOH B 373 1.57 REMARK 500 O GLU B 144 H2 HOH B 266 1.60 REMARK 500 O SER B 135 H1 HOH B 385 1.60 REMARK 500 OG SER B 195 O6' BMZ B 246 2.08 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 OD1 ASN B 87 H1 HOH A 467 4555 1.60 REMARK 500 O THR A 17 H1 HOH B 355 1545 1.60 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 B 91 NE2 HIS B 91 CD2 -0.067 REMARK 500 HIS B 99 NE2 HIS B 99 CD2 -0.067 REMARK 500 HIS B 165 NE2 HIS B 165 CD2 -0.071 REMARK 500 HIS B 233 NE2 HIS B 233 CD2 -0.068 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 CYS A 13 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 HIS B 37 N - CA - C ANGL. DEV. = -23.8 DEGREES REMARK 500 ARG B 70 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 116 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 166 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 LEU B 199 N - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 ARG B 206 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET B 207 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG B 217 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLY B 226 N - CA - C ANGL. DEV. = -16.0 DEGREES REMARK 500 ARG B 230 NE - CZ - NH2 ANGL. DEV. = -3.1 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 GLN B 27 59.21 -150.28 REMARK 500 VAL B 41 -72.64 -112.03 REMARK 500 SER B 54 -148.85 -153.36 REMARK 500 PRO B 60C 41.20 -73.99 REMARK 500 ASP B 93 20.23 96.34 REMARK 500 LEU B 97B -66.44 128.09 REMARK 500 MET B 126 119.90 -36.09 REMARK 500 LYS B 143 152.57 -45.92 REMARK 500 TYR B 171 -108.45 -112.05 REMARK 500 TRP B 186 43.73 35.84 REMARK 500 ASP B 189 -177.84 179.95 REMARK 500 GLN B 204 13.24 59.35 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 CIT B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMZ B 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C5X RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT INHIBITOR DBREF 1GI8 A 1 23 UNP P00749 UROK_HUMAN 156 178 DBREF 1GI8 B 16 242 UNP P00749 UROK_HUMAN 179 423 SEQADV 1GI8 ALA B 145 UNP P00749 ASN 322 CONFLICT SEQRES 1 A 23 LYS PRO SER SER PRO PRO GLU GLU LEU LYS PHE GLN CYS SEQRES 2 A 23 GLY GLN LYS THR LEU ARG PRO ARG PHE LYS SEQRES 1 B 245 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 B 245 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 B 245 VAL THR TYR VAL CYS GLY GLY SER LEU MET SER PRO CYS SEQRES 4 B 245 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 B 245 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 B 245 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 B 245 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 B 245 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 B 245 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 B 245 GLN THR ILE CYS LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 B 245 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 B 245 ALA SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 B 245 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 B 245 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 B 245 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 B 245 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 B 245 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 B 245 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 B 245 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR HET CIT B 1 18 HET CIT B 2 18 HET BMZ B 246 31 HETNAM CIT CITRIC ACID HETNAM BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 BMZ C14 H13 N4 O 1+ FORMUL 6 HOH *395(H2 O) HELIX 1 1 THR B 23 GLN B 27 5 5 HELIX 2 2 ALA B 55 PHE B 59 5 5 HELIX 3 3 LYS B 61 GLU B 62A 5 3 HELIX 4 4 SER B 164 GLN B 169 1 6 HELIX 5 5 TYR B 172 VAL B 176 5 5 HELIX 6 6 PHE B 234 THR B 242 1 9 SHEET 1 A 7 PHE B 30 ARG B 36 0 SHEET 2 A 7 VAL B 38 SER B 48 -1 O THR B 39 N ARG B 35 SHEET 3 A 7 TRP B 51 SER B 54 -1 O TRP B 51 N MET B 47 SHEET 4 A 7 ALA B 104 ARG B 109 -1 O ALA B 104 N SER B 54 SHEET 5 A 7 MET B 81 LEU B 90 -1 N GLU B 84 O ARG B 109 SHEET 6 A 7 TYR B 64 LEU B 68 -1 O TYR B 64 N VAL B 85 SHEET 7 A 7 PHE B 30 ARG B 36 -1 O ALA B 32 N TYR B 67 SHEET 1 B 2 SER B 95 ALA B 96 0 SHEET 2 B 2 HIS B 99 HIS B 100 -1 N HIS B 100 O SER B 95 SSBOND 1 CYS A 13 CYS B 122 1555 1555 2.02 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.02 SSBOND 3 CYS B 50 CYS B 111 1555 1555 2.02 SSBOND 4 CYS B 136 CYS B 201 1555 1555 2.02 SSBOND 5 CYS B 168 CYS B 182 1555 1555 2.02 SSBOND 6 CYS B 191 CYS B 220 1555 1555 2.01 LINK O6 CIT B 1 O6 CIT B 2 1555 1555 1.73 SITE 1 AC1 7 CIT B 2 TYR B 67 LYS B 82 SER B 164 SITE 2 AC1 7 HIS B 165 ARG B 166 HOH B 543 SITE 1 AC2 9 CIT B 1 ARG B 36 LYS B 82 LYS B 110A SITE 2 AC2 9 HIS B 165 ARG B 166 ARG B 230 HOH B 306 SITE 3 AC2 9 HOH B 383 SITE 1 AC3 14 HIS B 57 GLN B 185B SER B 190 CYS B 191 SITE 2 AC3 14 GLN B 192 SER B 195 VAL B 213 TRP B 215 SITE 3 AC3 14 GLY B 216 GLY B 219 GLY B 226 HOH B 477 SITE 4 AC3 14 HOH B 482 HOH B 488 CRYST1 82.200 48.770 67.020 90.00 113.53 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 0.012165 0.000000 0.005297 0.00000 SCALE2 0.000000 0.020504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016274 0.00000