HEADER HYDROLASE/HYDROLASE INHIBITOR 15-AUG-12 4GLY TITLE HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR UPA IN COMPLEX WITH THE TITLE 2 TWO-DISULFIDE BRIDGE PEPTIDE UK504 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 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 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: BICYCLIC PEPTIDE INHIBITOR UK504; COMPND 13 CHAIN: B; 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 STRAIN: 9606; SOURCE 6 GENE: PLAU; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK-293; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSECTAGA; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS SERINE PROTEASE, CHYMOTRYPSIN FOLD, UROKINASE-TYPE PLASMINOGEN KEYWDS 2 ACTIVATOR, BICYCLIC PEPTIDE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.A.BUTH,P.G.LEIMAN,S.CHEN,C.HEINIS REVDAT 3 13-SEP-23 4GLY 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4GLY 1 REMARK REVDAT 1 15-MAY-13 4GLY 0 JRNL AUTH S.CHEN,I.RENTERO REBOLLO,S.A.BUTH,J.MORALES-SANFRUTOS, JRNL AUTH 2 J.TOUATI,P.G.LEIMAN,C.HEINIS JRNL TITL BICYCLIC PEPTIDE LIGANDS PULLED OUT OF CYSTEINE-RICH PEPTIDE JRNL TITL 2 LIBRARIES. JRNL REF J.AM.CHEM.SOC. V. 135 6562 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23560397 JRNL DOI 10.1021/JA400461H REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 6.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 34197 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1784 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) : 1.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2528 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1400 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.27000 REMARK 3 B12 (A**2) : -0.08000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.923 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2150 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2910 ; 1.996 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.860 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.166 ;22.766 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;13.744 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;22.142 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1600 ; 0.013 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 2150 ; 5.640 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 84 ;52.906 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2329 ;20.461 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4GLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) IN (+ REMARK 200 --+) GEOMETRY AND A TOROIDAL REMARK 200 MIRROR (M2) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36222 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.518 REMARK 200 RESOLUTION RANGE LOW (A) : 29.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5 REMARK 200 STARTING MODEL: PDB ENTRY 2NWN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 5% PEG400, REMARK 280 0.05% SODIUM AZIDE, PH 4.6, 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 60.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.87196 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.36000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.40000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 34.87196 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.36000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.40000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 34.87196 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.36000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.74391 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.72000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.74391 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.72000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.74391 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 28.72000 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: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11560 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 400 REMARK 400 COMPOUND REMARK 400 BICYCLIC PEPTIDE INHIBITOR UK504 REMARK 400 REMARK 400 THE BICYCLIC PEPTIDE INHIBITOR UK504 IS CYCLIC PEPTIDE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BICYCLIC PEPTIDE INHIBITOR UK504 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 632 O HOH A 641 1.81 REMARK 500 NE2 GLN A 119 O HOH A 553 1.82 REMARK 500 OG1 THR A 39 O HOH A 681 1.95 REMARK 500 O HOH A 538 O HOH A 603 2.01 REMARK 500 CB CYS B 12 N NH2 B 14 2.03 REMARK 500 O HOH A 454 O HOH A 466 2.08 REMARK 500 NH2 ARG A 36 O HOH A 675 2.11 REMARK 500 O HOH A 538 O HOH A 594 2.13 REMARK 500 O HOH A 627 O HOH A 628 2.18 REMARK 500 ND2 ASN A 74 OE1 GLU A 153 2.18 REMARK 500 O ARG A 36 O HOH A 604 2.19 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 629 O HOH A 631 5455 2.17 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 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 CYS B 12 CB - CA - C ANGL. DEV. = 8.6 DEGREES REMARK 500 CYS B 12 CA - CB - SG ANGL. DEV. = 8.0 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 GLN A 27 66.26 -160.37 REMARK 500 SER A 54 -158.91 -150.75 REMARK 500 LEU A 97B -72.93 -156.48 REMARK 500 TYR A 171 -108.96 -93.24 REMARK 500 SER A 214 -54.79 -122.15 REMARK 500 CYS B 12 -111.88 -91.54 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 CYS B 12 LEU B 13 39.02 REMARK 500 REMARK 500 REMARK: NULL 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 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 25 OE1 REMARK 620 2 GLU A 25 OE2 39.7 REMARK 620 3 SER A 71 OG 90.9 129.6 REMARK 620 4 HOH A 462 O 124.0 84.5 141.3 REMARK 620 5 HOH A 563 O 113.9 114.8 90.6 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 48 OG REMARK 620 2 HOH A 593 O 120.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P6G A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE REMARK 800 INHIBITOR UK504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QN7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN (UPA) COMPLEXED WITH A DIFFERENT PEPTIDE INHIBITOR DBREF 4GLY A 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4GLY B 1 14 PDB 4GLY 4GLY 1 14 SEQADV 4GLY ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4GLY GLN A 145 UNP P00749 ASN 322 ENGINEERED MUTATION SEQRES 1 A 245 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 A 245 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 A 245 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 A 245 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 A 245 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 A 245 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 A 245 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 A 245 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 A 245 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 A 245 GLN THR ILE ALA LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 A 245 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 A 245 GLN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 A 245 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 A 245 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 A 245 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 A 245 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 A 245 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 A 245 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 A 245 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR SEQRES 1 B 14 CYS CYS LEU GLY ARG GLY CYS GLU ASN HIS ARG CYS LEU SEQRES 2 B 14 NH2 HET NH2 B 14 1 HET SO4 A 301 5 HET SO4 A 302 5 HET NA A 303 1 HET CL A 304 1 HET NA A 305 1 HET CL A 306 1 HET CL A 307 1 HET SO4 A 308 5 HET SO4 A 309 5 HET P6G A 310 19 HET GOL A 311 6 HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM P6G HEXAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN P6G POLYETHYLENE GLYCOL PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NH2 H2 N FORMUL 3 SO4 4(O4 S 2-) FORMUL 5 NA 2(NA 1+) FORMUL 6 CL 3(CL 1-) FORMUL 12 P6G C12 H26 O7 FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *310(H2 O) HELIX 1 1 THR A 23 GLN A 27 5 5 HELIX 2 2 ALA A 55 PHE A 59 5 5 HELIX 3 3 LYS A 61 GLU A 62A 5 3 HELIX 4 4 SER A 164 GLN A 169 1 6 HELIX 5 5 TYR A 172 VAL A 176 5 5 HELIX 6 6 PHE A 234 THR A 242 1 9 SHEET 1 A 8 GLU A 20 PHE A 21 0 SHEET 2 A 8 LYS A 156 ILE A 163 -1 O MET A 157 N GLU A 20 SHEET 3 A 8 MET A 180 ALA A 184 -1 O CYS A 182 N ILE A 163 SHEET 4 A 8 GLY A 226 ARG A 230 -1 O TYR A 228 N LEU A 181 SHEET 5 A 8 ARG A 206 TRP A 215 -1 N TRP A 215 O VAL A 227 SHEET 6 A 8 PRO A 198 LEU A 203 -1 N LEU A 199 O GLY A 211 SHEET 7 A 8 SER A 135 GLY A 140 -1 N GLU A 137 O VAL A 200 SHEET 8 A 8 LYS A 156 ILE A 163 -1 O VAL A 160 N CYS A 136 SHEET 1 B 7 PHE A 30 ARG A 36 0 SHEET 2 B 7 VAL A 38 SER A 48 -1 O VAL A 41 N ILE A 33 SHEET 3 B 7 TRP A 51 SER A 54 -1 O ILE A 53 N SER A 45 SHEET 4 B 7 ALA A 104 ARG A 109 -1 O LEU A 106 N VAL A 52 SHEET 5 B 7 MET A 81 LEU A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 B 7 TYR A 64 LEU A 68 -1 N VAL A 66 O PHE A 83 SHEET 7 B 7 PHE A 30 ARG A 36 -1 N TYR A 34 O ILE A 65 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.09 SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.05 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.02 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.06 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.12 SSBOND 6 CYS B 1 CYS B 12 1555 1555 2.06 SSBOND 7 CYS B 2 CYS B 7 1555 1555 2.09 LINK C LEU B 13 N NH2 B 14 1555 1555 1.26 LINK OE1 GLU A 25 NA NA A 305 1555 1555 3.10 LINK OE2 GLU A 25 NA NA A 305 1555 1555 3.13 LINK OG SER A 48 NA NA A 303 1555 1555 2.87 LINK OG SER A 71 NA NA A 305 1555 1555 3.12 LINK NA NA A 303 O HOH A 593 1555 1555 2.22 LINK NA NA A 305 O HOH A 462 1555 1555 3.00 LINK NA NA A 305 O HOH A 563 1555 1555 2.81 SITE 1 AC1 9 ALA A 96 ASP A 97 THR A 97A TYR A 127 SITE 2 AC1 9 THR A 178 LYS A 179 HIS A 233 HOH A 459 SITE 3 AC1 9 HOH A 507 SITE 1 AC2 7 LYS A 62 ASN A 87 GLN A 170 PRO A 170A SITE 2 AC2 7 HIS A 170B HOH A 433 HOH A 525 SITE 1 AC3 4 SER A 48 PRO A 49 CYS A 50 HOH A 593 SITE 1 AC4 4 ARG A 217 GLY A 218 HOH A 688 GLY B 4 SITE 1 AC5 6 GLU A 25 SER A 71 THR A 77 HOH A 462 SITE 2 AC5 6 HOH A 481 HOH A 563 SITE 1 AC6 4 ILE A 163 HIS A 165 LEU A 181 CYS A 182 SITE 1 AC7 4 ASN A 101 HOH A 498 HOH A 600 HOH A 648 SITE 1 AC8 3 ARG A 35 HIS A 37 ARG A 37A SITE 1 AC9 5 SER A 164 HIS A 165 HOH A 436 HOH A 492 SITE 2 AC9 5 HOH A 601 SITE 1 BC1 11 VAL A 38 THR A 39 TYR A 40 ASN A 74 SITE 2 BC1 11 SER A 135 TYR A 149 TYR A 151 SER A 202 SITE 3 BC1 11 HOH A 458 HOH A 474 HOH A 605 SITE 1 BC2 6 GLU A 167 GLN A 170 TYR A 171 LYS A 223 SITE 2 BC2 6 ASP A 223A HOH A 623 SITE 1 BC3 38 ARG A 35 VAL A 41 HIS A 57 CYS A 58 SITE 2 BC3 38 ASP A 60A TYR A 60B TYR A 64 ASP A 97 SITE 3 BC3 38 THR A 97A LEU A 97B HIS A 99 ASP A 189 SITE 4 BC3 38 SER A 190 GLN A 192 GLY A 193 SER A 195 SITE 5 BC3 38 SER A 214 GLY A 216 ARG A 217 GLY A 218 SITE 6 BC3 38 CYS A 220 LYS A 224 GLY A 226 CL A 304 SITE 7 BC3 38 HOH A 423 HOH A 478 HOH A 550 HOH A 580 SITE 8 BC3 38 HOH A 685 HOH B 101 HOH B 102 HOH B 103 SITE 9 BC3 38 HOH B 104 HOH B 106 HOH B 108 HOH B 110 SITE 10 BC3 38 HOH B 111 HOH B 113 CRYST1 120.800 120.800 43.080 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 0.008278 0.004779 0.000000 0.00000 SCALE2 0.000000 0.009559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023213 0.00000