HEADER HYDROLASE 27-JUL-09 3IG6 TITLE LOW MOLECULAR WEIGTH HUMAN UROKINASE TYPE PLASMINOGEN ACTIVATOR 2-[6- TITLE 2 (3'-AMINOMETHYL-BIPHENYL-3-YLOXY)-4-(3-DIMETHYLAMINO-PYRROLIDIN-1- TITLE 3 YL)-3,5-DIFLUORO-PYRIDIN-2-YLOXY]-4-DIMETHYLAMINO-BENZOIC ACID TITLE 4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: FRAGMENT OF LIGHT CHAIN; COMPND 5 SYNONYM: U-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN COMPND 6 ACTIVATOR LONG CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR SHORT COMPND 7 CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 8 EC: 3.4.21.73; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 12 CHAIN: B, D; COMPND 13 FRAGMENT: CATALYTIC DOMAIN; COMPND 14 SYNONYM: U-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN COMPND 15 ACTIVATOR LONG CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR SHORT COMPND 16 CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 17 EC: 3.4.21.73; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLAU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: PLAU; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SELECTIVE, S1 SITE INHIBITOR, STRUCTURE-BASED DRUG DESIGN, UROKINASE, KEYWDS 2 BLOOD COAGULATION, DISULFIDE BOND, EGF-LIKE DOMAIN, FIBRINOLYSIS, KEYWDS 3 GLYCOPROTEIN, HYDROLASE, KRINGLE, PHARMACEUTICAL, PHOSPHOPROTEIN, KEYWDS 4 PLASMINOGEN ACTIVATION, POLYMORPHISM, PROTEASE, SECRETED, SERINE KEYWDS 5 PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR M.ADLER,M.WHITLOW REVDAT 4 30-OCT-24 3IG6 1 REMARK REVDAT 3 06-SEP-23 3IG6 1 REMARK REVDAT 2 16-NOV-11 3IG6 1 VERSN HETATM REVDAT 1 13-OCT-09 3IG6 0 JRNL AUTH C.W.WEST,M.ADLER,D.ARNAIZ,D.CHEN,K.CHU,G.GUALTIERI,E.HO, JRNL AUTH 2 C.HUWE,D.LIGHT,G.PHILLIPS,R.PULK,D.SUKOVICH,M.WHITLOW, JRNL AUTH 3 S.YUAN,J.BRYANT JRNL TITL IDENTIFICATION OF ORALLY BIOAVAILABLE, NON-AMIDINE JRNL TITL 2 INHIBITORS OF UROKINASE PLASMINOGEN ACTIVATOR (UPA) JRNL REF BIOORG.MED.CHEM.LETT. V. 19 5712 2009 JRNL REFN ISSN 0960-894X JRNL PMID 19703768 JRNL DOI 10.1016/J.BMCL.2009.08.008 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 132827.960 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 42641 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1684 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2250 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2240 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1849 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0060 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 46597 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5887 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 232 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3939 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.50000 REMARK 3 B22 (A**2) : 1.59000 REMARK 3 B33 (A**2) : -3.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.94000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.660 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.060 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 50.94 REMARK 3 REMARK 3 NCS MODEL : NONE 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 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : WATER_REP.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : 438.PAR REMARK 3 PARAMETER FILE 5 : &_1_PARAMETER_INFILE_5 REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : 438.TOP REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47497 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.450 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05350 REMARK 200 FOR THE DATA SET : 15.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.26 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24400 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX REMARK 200 STARTING MODEL: PDB ENTRY 1LMW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.4 G/L, 1 MM LIGAND IN 50 MM TRIS PH REMARK 280 7.4, 5 MM NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 839 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 9 REMARK 465 LYS A 10 REMARK 465 PHE A 11 REMARK 465 GLN A 12 REMARK 465 LYS A 16 REMARK 465 THR A 17 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 465 LYS B 243 REMARK 465 GLU B 244 REMARK 465 GLU B 245 REMARK 465 ASN B 246 REMARK 465 GLY B 247 REMARK 465 LEU B 248 REMARK 465 ALA B 249 REMARK 465 LEU B 250 REMARK 465 LYS C 1 REMARK 465 PRO C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 PRO C 5 REMARK 465 PRO C 6 REMARK 465 GLU C 7 REMARK 465 GLU C 8 REMARK 465 LEU C 9 REMARK 465 ARG C 19 REMARK 465 PRO C 20 REMARK 465 ARG C 21 REMARK 465 PHE C 22 REMARK 465 LYS C 23 REMARK 465 ARG D 36T REMARK 465 GLY D 36U REMARK 465 GLY D 36V REMARK 465 GLU D 244 REMARK 465 GLU D 245 REMARK 465 ASN D 246 REMARK 465 GLY D 247 REMARK 465 LEU D 248 REMARK 465 ALA D 249 REMARK 465 LEU D 250 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 GLN C 15 CG CD OE1 NE2 REMARK 470 LYS D 243 CG CD CE NZ 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 D 859 O HOH D 859 2556 1.08 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 VAL B 41 -66.86 -108.12 REMARK 500 SER B 54 -154.86 -149.67 REMARK 500 ASP B 97 -145.92 -96.92 REMARK 500 TYR B 171 -104.14 -98.83 REMARK 500 SER B 214 -59.30 -124.77 REMARK 500 VAL D 41 -62.38 -106.89 REMARK 500 SER D 54 -154.85 -147.59 REMARK 500 PRO D 60C 37.20 -80.65 REMARK 500 ASP D 97 -148.62 -105.10 REMARK 500 LEU D 97B -61.40 -130.00 REMARK 500 TYR D 171 -102.59 -91.77 REMARK 500 SER D 214 -58.17 -123.38 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 438 B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 438 D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 450 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SQA RELATED DB: PDB REMARK 900 UPA WITH INHIBITOR REMARK 900 RELATED ID: 1W14 RELATED DB: PDB REMARK 900 UPA WITH INHIBITOR REMARK 900 RELATED ID: 1VJA RELATED DB: PDB REMARK 900 UPA WITH INHIBITOR REMARK 900 RELATED ID: 1OWJ RELATED DB: PDB REMARK 900 UPA WITH INHIBITOR REMARK 900 RELATED ID: 1F92 RELATED DB: PDB REMARK 900 UPA WITH INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE ACTIVE FORM OF UROKINASE IS CREATED BY A REMARK 999 PROTEOLYTIC CLIP, THUS IT HAS TWO CHAINS DBREF 3IG6 A 1 23 UNP Q5SWW9 UROK_HUMAN 156 178 DBREF 3IG6 B 16 250 UNP Q5SWW9 UROK_HUMAN 179 431 DBREF 3IG6 C 1 23 UNP Q5SWW9 UROK_HUMAN 156 178 DBREF 3IG6 D 16 250 UNP Q5SWW9 UROK_HUMAN 179 431 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 253 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 B 253 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 B 253 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 B 253 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 B 253 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 B 253 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 B 253 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 B 253 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 B 253 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 B 253 GLN THR ILE CYS LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 B 253 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 B 253 ASN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 B 253 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 B 253 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 B 253 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 B 253 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 B 253 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 B 253 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 B 253 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS GLU SEQRES 20 B 253 GLU ASN GLY LEU ALA LEU SEQRES 1 C 23 LYS PRO SER SER PRO PRO GLU GLU LEU LYS PHE GLN CYS SEQRES 2 C 23 GLY GLN LYS THR LEU ARG PRO ARG PHE LYS SEQRES 1 D 253 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 D 253 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 D 253 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 D 253 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 D 253 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 D 253 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 D 253 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 D 253 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 D 253 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 D 253 GLN THR ILE CYS LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 D 253 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 D 253 ASN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 D 253 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 D 253 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 D 253 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 D 253 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 D 253 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 D 253 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 D 253 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS GLU SEQRES 20 D 253 GLU ASN GLY LEU ALA LEU HET 438 B 400 44 HET 438 D 401 44 HET PO4 D 450 5 HETNAM 438 2-[(6-{[3'-(AMINOMETHYL)BIPHENYL-3-YL]OXY}-4-[(3R)-3- HETNAM 2 438 (DIMETHYLAMINO)PYRROLIDIN-1-YL]-3,5-DIFLUOROPYRIDIN-2- HETNAM 3 438 YL)OXY]-4-(DIMETHYLAMINO)BENZOIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 5 438 2(C33 H35 F2 N5 O4) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *227(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 HELIX 7 7 THR D 23 GLN D 27 5 5 HELIX 8 8 ALA D 55 PHE D 59 5 5 HELIX 9 9 LYS D 61 GLU D 62A 5 3 HELIX 10 10 SER D 164 GLN D 169 1 6 HELIX 11 11 TYR D 172 VAL D 176 5 5 HELIX 12 12 PHE D 234 LYS D 243 1 10 SHEET 1 A 8 GLU B 20 PHE B 21 0 SHEET 2 A 8 LYS B 156 ILE B 163 -1 O MET B 157 N GLU B 20 SHEET 3 A 8 MET B 180 ALA B 184 -1 O CYS B 182 N ILE B 163 SHEET 4 A 8 GLY B 226 ARG B 230 -1 O TYR B 228 N LEU B 181 SHEET 5 A 8 ARG B 206 TRP B 215 -1 N TRP B 215 O VAL B 227 SHEET 6 A 8 PRO B 198 LEU B 203 -1 N LEU B 203 O ARG B 206 SHEET 7 A 8 SER B 135 GLY B 140 -1 N GLU B 137 O VAL B 200 SHEET 8 A 8 LYS B 156 ILE B 163 -1 O VAL B 160 N CYS B 136 SHEET 1 B 7 PHE B 30 ARG B 36 0 SHEET 2 B 7 VAL B 38 SER B 48 -1 O VAL B 41 N ILE B 33 SHEET 3 B 7 TRP B 51 SER B 54 -1 O ILE B 53 N SER B 45 SHEET 4 B 7 ALA B 104 ARG B 109 -1 O LEU B 106 N VAL B 52 SHEET 5 B 7 MET B 81 LEU B 90 -1 N GLU B 84 O ARG B 109 SHEET 6 B 7 TYR B 64 LEU B 68 -1 N VAL B 66 O PHE B 83 SHEET 7 B 7 PHE B 30 ARG B 36 -1 N TYR B 34 O ILE B 65 SHEET 1 C 2 SER B 95 ALA B 96 0 SHEET 2 C 2 HIS B 99 HIS B 100 -1 O HIS B 100 N SER B 95 SHEET 1 D 8 GLU D 20 PHE D 21 0 SHEET 2 D 8 LYS D 156 ILE D 163 -1 O MET D 157 N GLU D 20 SHEET 3 D 8 MET D 180 ALA D 184 -1 O CYS D 182 N ILE D 163 SHEET 4 D 8 GLY D 226 ARG D 230 -1 O TYR D 228 N LEU D 181 SHEET 5 D 8 ARG D 206 TRP D 215 -1 N TRP D 215 O VAL D 227 SHEET 6 D 8 PRO D 198 LEU D 203 -1 N LEU D 203 O ARG D 206 SHEET 7 D 8 SER D 135 GLY D 140 -1 N GLU D 137 O VAL D 200 SHEET 8 D 8 LYS D 156 ILE D 163 -1 O VAL D 160 N CYS D 136 SHEET 1 E 7 PHE D 30 ARG D 35 0 SHEET 2 E 7 THR D 39 SER D 48 -1 O THR D 39 N ARG D 35 SHEET 3 E 7 TRP D 51 SER D 54 -1 O ILE D 53 N SER D 45 SHEET 4 E 7 ALA D 104 ARG D 109 -1 O LEU D 106 N VAL D 52 SHEET 5 E 7 MET D 81 LEU D 90 -1 N ILE D 89 O LEU D 105 SHEET 6 E 7 TYR D 64 LEU D 68 -1 N VAL D 66 O PHE D 83 SHEET 7 E 7 PHE D 30 ARG D 35 -1 N TYR D 34 O ILE D 65 SHEET 1 F 2 SER D 95 ALA D 96 0 SHEET 2 F 2 HIS D 99 HIS D 100 -1 O HIS D 100 N SER D 95 SSBOND 1 CYS A 13 CYS B 122 1555 1555 2.03 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 3 CYS B 50 CYS B 111 1555 1555 2.04 SSBOND 4 CYS B 136 CYS B 201 1555 1555 2.04 SSBOND 5 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 6 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 7 CYS C 13 CYS D 122 1555 1555 2.04 SSBOND 8 CYS D 42 CYS D 58 1555 1555 2.03 SSBOND 9 CYS D 50 CYS D 111 1555 1555 2.03 SSBOND 10 CYS D 136 CYS D 201 1555 1555 2.03 SSBOND 11 CYS D 168 CYS D 182 1555 1555 2.04 SSBOND 12 CYS D 191 CYS D 220 1555 1555 2.04 SITE 1 AC1 26 VAL B 41 HIS B 57 ALA B 96 LEU B 97B SITE 2 AC1 26 ALA B 98 HIS B 99 ASP B 189 SER B 190 SITE 3 AC1 26 CYS B 191 GLN B 192 GLY B 193 SER B 195 SITE 4 AC1 26 GLY B 216 GLY B 218 CYS B 220 HOH B 717 SITE 5 AC1 26 HOH B 720 ILE D 60 ASP D 60A LYS D 92 SITE 6 AC1 26 TYR D 94 SER D 95 ALA D 96 HOH D 675 SITE 7 AC1 26 HOH D 764 HOH D 851 SITE 1 AC2 16 TYR B 149 LEU B 150 SER D 146 ASP D 189 SITE 2 AC2 16 SER D 190 CYS D 191 GLN D 192 SER D 195 SITE 3 AC2 16 TRP D 215 GLY D 216 ARG D 217 GLY D 218 SITE 4 AC2 16 CYS D 220 PO4 D 450 HOH D 619 HOH D 718 SITE 1 AC3 6 HIS D 57 GLN D 192 GLY D 193 SER D 195 SITE 2 AC3 6 438 D 401 HOH D 739 CRYST1 70.855 52.294 72.580 90.00 90.23 90.00 P 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 0.014113 0.000000 0.000058 0.00000 SCALE2 0.000000 0.019123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013778 0.00000 CONECT 6 985 CONECT 270 382 CONECT 319 902 CONECT 382 270 CONECT 902 319 CONECT 985 6 CONECT 1092 1629 CONECT 1352 1482 CONECT 1482 1352 CONECT 1566 1761 CONECT 1629 1092 CONECT 1761 1566 CONECT 1989 2969 CONECT 2254 2366 CONECT 2303 2886 CONECT 2366 2254 CONECT 2886 2303 CONECT 2969 1989 CONECT 3076 3613 CONECT 3336 3466 CONECT 3466 3336 CONECT 3550 3745 CONECT 3613 3076 CONECT 3745 3550 CONECT 3944 3945 CONECT 3945 3944 3950 CONECT 3946 3947 3951 3952 CONECT 3947 3946 3948 CONECT 3948 3947 3949 CONECT 3949 3948 3950 CONECT 3950 3945 3949 3951 CONECT 3951 3946 3950 CONECT 3952 3946 3953 3957 CONECT 3953 3952 3954 CONECT 3954 3953 3955 3958 CONECT 3955 3954 3956 CONECT 3956 3955 3957 CONECT 3957 3952 3956 CONECT 3958 3954 3960 CONECT 3959 3960 3964 CONECT 3960 3958 3959 3961 CONECT 3961 3960 3962 3965 CONECT 3962 3961 3963 3966 CONECT 3963 3962 3964 3967 CONECT 3964 3959 3963 3968 CONECT 3965 3961 CONECT 3966 3962 3981 3984 CONECT 3967 3963 CONECT 3968 3964 3969 CONECT 3969 3968 3970 3975 CONECT 3970 3969 3971 CONECT 3971 3970 3972 3973 CONECT 3972 3971 3979 3980 CONECT 3973 3971 3974 CONECT 3974 3973 3975 CONECT 3975 3969 3974 3976 CONECT 3976 3975 3977 3978 CONECT 3977 3976 CONECT 3978 3976 CONECT 3979 3972 CONECT 3980 3972 CONECT 3981 3966 3982 CONECT 3982 3981 3983 3985 CONECT 3983 3982 3984 CONECT 3984 3966 3983 CONECT 3985 3982 3986 3987 CONECT 3986 3985 CONECT 3987 3985 CONECT 3988 3989 CONECT 3989 3988 3994 CONECT 3990 3991 3995 3996 CONECT 3991 3990 3992 CONECT 3992 3991 3993 CONECT 3993 3992 3994 CONECT 3994 3989 3993 3995 CONECT 3995 3990 3994 CONECT 3996 3990 3997 4001 CONECT 3997 3996 3998 CONECT 3998 3997 3999 4002 CONECT 3999 3998 4000 CONECT 4000 3999 4001 CONECT 4001 3996 4000 CONECT 4002 3998 4004 CONECT 4003 4004 4008 CONECT 4004 4002 4003 4005 CONECT 4005 4004 4006 4009 CONECT 4006 4005 4007 4010 CONECT 4007 4006 4008 4011 CONECT 4008 4003 4007 4012 CONECT 4009 4005 CONECT 4010 4006 4025 4028 CONECT 4011 4007 CONECT 4012 4008 4013 CONECT 4013 4012 4014 4019 CONECT 4014 4013 4015 CONECT 4015 4014 4016 4017 CONECT 4016 4015 4023 4024 CONECT 4017 4015 4018 CONECT 4018 4017 4019 CONECT 4019 4013 4018 4020 CONECT 4020 4019 4021 4022 CONECT 4021 4020 CONECT 4022 4020 CONECT 4023 4016 CONECT 4024 4016 CONECT 4025 4010 4026 CONECT 4026 4025 4027 4029 CONECT 4027 4026 4028 CONECT 4028 4010 4027 CONECT 4029 4026 4030 4031 CONECT 4030 4029 CONECT 4031 4029 CONECT 4032 4033 4034 4035 4036 CONECT 4033 4032 CONECT 4034 4032 CONECT 4035 4032 CONECT 4036 4032 MASTER 405 0 3 12 34 0 13 6 4259 4 117 44 END