HEADER HYDROLASE/HYDROLASE INHIBITOR 08-FEB-11 3QN7 TITLE POTENT AND SELECTIVE BICYCLIC PEPTIDE INHIBITOR (UK18) OF HUMAN TITLE 2 UROKINASE-TYPE PLASMINOGEN ACTIVATOR(UPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UROKINASE-TYPE PLASMINOGEN ACTIVATOR COMPND 5 CHAIN B; COMPND 6 SYNONYM: U-PLASMINOGEN ACTIVATOR, UPA; COMPND 7 EC: 3.4.21.73; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: BICYCLIC PEPTIDE INHIBITOR; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: UK18; COMPND 14 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HUMAN EMBRYONIC KIDNEY CELLS (HEK-293); SOURCE 10 EXPRESSION_SYSTEM_CELL: MAMMALIAN CELLS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PSECTAGA; SOURCE 13 MOL_ID: 2; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS BICYCLIC PEPTIDE INHIBITOR, CHYMOTRYPSIN FOLD, SERINE PROTEASE, KEYWDS 2 UROKINASE RECEPTOR (UPAR), EXTRACELLULAR, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.ANGELINI,L.CENDRON,J.TOUATI,G.WINTER,G.ZANOTTI,C.HEINIS REVDAT 3 01-NOV-23 3QN7 1 REMARK SEQADV LINK REVDAT 2 10-APR-13 3QN7 1 JRNL REVDAT 1 15-FEB-12 3QN7 0 JRNL AUTH A.ANGELINI,L.CENDRON,S.CHEN,J.TOUATI,G.WINTER,G.ZANOTTI, JRNL AUTH 2 C.HEINIS JRNL TITL BICYCLIC PEPTIDE INHIBITOR REVEALS LARGE CONTACT INTERFACE JRNL TITL 2 WITH A PROTEASE TARGET JRNL REF ACS CHEM.BIOL. V. 7 817 2012 JRNL REFN ISSN 1554-8929 JRNL PMID 22304751 JRNL DOI 10.1021/CB200478T REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.ZHAO,C.YUAN,T.WIND,Z.HUANG,P.A.ANDREASEN,M.HUANG REMARK 1 TITL STRUCTURAL BASIS OF SPECIFICITY OF A PEPTIDYL UROKINASE REMARK 1 TITL 2 INHIBITOR, UPAIN-1 REMARK 1 REF J.STRUCT.BIOL. V. 160 1 2007 REMARK 1 REFN ISSN 1047-8477 REMARK 1 PMID 17692534 REMARK 1 DOI 10.1016/J.JSB.2007.06.003 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.SPRAGGON,C.PHILLIPS,U.K.NOWAK,C.P.PONTING,D.SAUNDERS, REMARK 1 AUTH 2 C.M.DOBSON,D.I.STUART,E.Y.JONES REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN REMARK 1 TITL 2 UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 1 REF STRUCTURE V. 3 681 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 8591045 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17487 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) : 0.195 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 946 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1313 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 1.44000 REMARK 3 B12 (A**2) : -0.48000 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): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.495 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2113 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2862 ; 1.900 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 7.462 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;27.911 ;22.903 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 354 ;16.772 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.594 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1602 ; 0.009 ; 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): 1292 ; 1.329 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2085 ; 2.344 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 821 ; 3.220 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 777 ; 4.940 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QN7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : TOROIDAL FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 2NWN.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.05M SODIUM REMARK 280 CITRATE, 5%(V/V) PEG 400, PH 4.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.62500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.00186 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.24000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.62500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 35.00186 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.24000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.62500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 35.00186 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.24000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.00372 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.48000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 70.00372 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.48000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 70.00372 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 28.48000 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: 1590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 246 REMARK 465 GLU A 247 REMARK 465 GLU A 248 REMARK 465 ASN A 249 REMARK 465 GLY A 250 REMARK 465 LEU A 251 REMARK 465 ALA A 252 REMARK 465 LEU A 253 REMARK 465 GLY B 17 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 O HOH A 347 O HOH A 351 1.93 REMARK 500 OE1 GLU A 77 O HOH A 361 2.11 REMARK 500 O HOH A 270 O HOH A 337 2.12 REMARK 500 O GLN A 130 OG1 THR A 133 2.18 REMARK 500 O HOH A 52 O HOH A 299 2.18 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 A 318 O HOH A 326 6454 2.05 REMARK 500 O HOH A 312 O HOH A 358 6455 2.09 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 MET A 74 CA - CB - CG ANGL. DEV. = 10.8 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 ARG A 23A -54.78 114.34 REMARK 500 SER A 26D -117.74 43.61 REMARK 500 SER A 43 -155.01 -153.21 REMARK 500 PRO A 52C 28.36 -79.89 REMARK 500 ASP A 90 -141.74 -82.00 REMARK 500 THR A 91A -71.40 -54.30 REMARK 500 TYR A 172 -102.50 -100.49 REMARK 500 SER A 217 -61.11 -125.23 REMARK 500 ASP A 226A 16.15 59.56 REMARK 500 CYS B 2 -137.64 52.37 REMARK 500 SER B 14 118.51 120.72 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 SER B 3 ARG B 4 -144.90 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 ZBR B 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE REMARK 800 INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LMW RELATED DB: PDB REMARK 900 HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 RELATED ID: 2NWN RELATED DB: PDB REMARK 900 HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) IN COMPLEX WITH A REMARK 900 BICYCLIC PEPTIDE INHIBITOR (UK18) DBREF 3QN7 A 1 253 UNP P00749 UROK_HUMAN 179 431 DBREF 3QN7 B 1 17 PDB 3QN7 3QN7 1 17 SEQADV 3QN7 ALA A 121 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 3QN7 GLN A 144 UNP P00749 ASN 322 ENGINEERED MUTATION SEQRES 1 A 253 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 A 253 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 A 253 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 A 253 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 A 253 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 A 253 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 A 253 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 A 253 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 A 253 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 A 253 GLN THR ILE ALA LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 A 253 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 A 253 GLN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 A 253 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 A 253 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 A 253 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 A 253 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 A 253 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 A 253 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 A 253 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS GLU SEQRES 20 A 253 GLU ASN GLY LEU ALA LEU SEQRES 1 B 17 ALA CYS SER ARG TYR GLU VAL ASP CYS ARG GLY ARG GLY SEQRES 2 B 17 SER ALA CYS GLY HET ZBR B 18 9 HETNAM ZBR 1,3,5-TRIS(BROMOMETHYL)BENZENE FORMUL 3 ZBR C9 H9 BR3 FORMUL 4 HOH *132(H2 O) HELIX 1 1 THR A 8 GLN A 12 5 5 HELIX 2 2 ALA A 44 PHE A 48 5 5 HELIX 3 3 LYS A 53 GLU A 55A 5 3 HELIX 4 4 SER A 163 GLN A 168 1 6 HELIX 5 5 PHE A 237 HIS A 244 1 8 SHEET 1 A 8 GLU A 5 PHE A 6 0 SHEET 2 A 8 LYS A 155 ILE A 162 -1 O MET A 156 N GLU A 5 SHEET 3 A 8 MET A 181 ALA A 185 -1 O ALA A 185 N LYS A 160 SHEET 4 A 8 GLY A 229 ARG A 233 -1 O TYR A 231 N LEU A 182 SHEET 5 A 8 ARG A 209 TRP A 218 -1 N TRP A 218 O VAL A 230 SHEET 6 A 8 PRO A 201 LEU A 206 -1 N CYS A 204 O THR A 211 SHEET 7 A 8 SER A 134 GLY A 139 -1 N GLU A 136 O VAL A 203 SHEET 8 A 8 LYS A 155 ILE A 162 -1 O VAL A 159 N CYS A 135 SHEET 1 B 7 PHE A 15 ARG A 21 0 SHEET 2 B 7 VAL A 27 SER A 37 -1 O VAL A 30 N ILE A 18 SHEET 3 B 7 TRP A 40 SER A 43 -1 O ILE A 42 N SER A 34 SHEET 4 B 7 ALA A 99 ARG A 104 -1 O LEU A 101 N VAL A 41 SHEET 5 B 7 MET A 74 LEU A 83 -1 N ILE A 82 O LEU A 100 SHEET 6 B 7 TYR A 57 LEU A 61 -1 N LEU A 61 O MET A 74 SHEET 7 B 7 PHE A 15 ARG A 21 -1 N TYR A 19 O ILE A 58 SHEET 1 C 2 SER A 88 ALA A 89 0 SHEET 2 C 2 HIS A 94 HIS A 95 -1 O HIS A 95 N SER A 88 SSBOND 1 CYS A 31 CYS A 47 1555 1555 2.06 SSBOND 2 CYS A 39 CYS A 110 1555 1555 2.03 SSBOND 3 CYS A 135 CYS A 204 1555 1555 2.06 SSBOND 4 CYS A 167 CYS A 183 1555 1555 2.06 SSBOND 5 CYS A 194 CYS A 222 1555 1555 2.09 LINK SG CYS B 2 C9 ZBR B 18 1555 1555 1.80 LINK SG CYS B 9 C7 ZBR B 18 1555 1555 1.81 LINK SG CYS B 16 C8 ZBR B 18 1555 1555 1.73 CISPEP 1 HIS A 22 ARG A 23A 0 0.84 CISPEP 2 ARG A 23A GLY A 24B 0 16.86 CISPEP 3 GLY A 24B GLY A 25C 0 8.24 CISPEP 4 GLU A 107B GLY A 108C 0 15.97 CISPEP 5 GLY B 13 SER B 14 0 15.14 SITE 1 AC1 6 ASP A 50A CYS B 2 ARG B 4 CYS B 9 SITE 2 AC1 6 ARG B 10 CYS B 16 SITE 1 AC2 33 ARG A 20 HIS A 22 ARG A 23A GLY A 24B SITE 2 AC2 33 GLY A 25C TYR A 29 VAL A 30 CYS A 31 SITE 3 AC2 33 HIS A 46 ILE A 49 ASP A 50A TYR A 51B SITE 4 AC2 33 HIS A 94 TYR A 150 ASP A 192 SER A 193 SITE 5 AC2 33 GLN A 195 GLY A 196 SER A 198 GLY A 219 SITE 6 AC2 33 GLY A 221 CYS A 222 LYS A 227 GLY A 229 SITE 7 AC2 33 HOH A 269 HOH A 304 HOH A 356 ZBR B 18 SITE 8 AC2 33 HOH B 19 HOH B 72 HOH B 85 HOH B 103 SITE 9 AC2 33 HOH B 108 CRYST1 121.250 121.250 42.720 90.00 90.00 120.00 H 3 9 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 0.008247 0.004762 0.000000 0.00000 SCALE2 0.000000 0.009523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023408 0.00000