PDB Short entry for 4MNY HEADER HYDROLASE/HYDROLASE INHIBITOR 11-SEP-13 4MNY TITLE CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) TITLE 2 COMPLEXED WITH BICYCLIC PEPTIDE UK903 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 179-423); COMPND 5 SYNONYM: U-PLASMINOGEN ACTIVATOR, UPA; COMPND 6 EC: 3.4.21.73; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: BICYCLIC PEPTIDE UK903; COMPND 11 CHAIN: C, D; COMPND 12 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: 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 OTHER_DETAILS: MODIFIED WITH N,N',N''-(BENZENE-1,3,5-TRIYL)TRIS(2- SOURCE 15 BROMOACETAMIDE) (TBAB) KEYWDS COMPETITIVE INHIBITOR, BICYCLIC PEPTIDE, INHIBITOR, PROTEASE, N, N', KEYWDS 2 N''-(BENZENE-1, 3, 5-TRIYL)TRIS(2-BROMOACETAMIDE) (TBAB) KEYWDS 3 CYCLIZATION, EXTRACELLULAR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,F.POJER,C.HEINIS REVDAT 3 15-NOV-17 4MNY 1 REMARK REVDAT 2 26-FEB-14 4MNY 1 JRNL REVDAT 1 05-FEB-14 4MNY 0 JRNL AUTH S.CHEN,D.BERTOLDO,A.ANGELINI,F.POJER,C.HEINIS JRNL TITL PEPTIDE LIGANDS STABILIZED BY SMALL MOLECULES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 1602 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 24453110 JRNL DOI 10.1002/ANIE.201309459 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 53950 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2847 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3506 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : -1.14000 REMARK 3 B33 (A**2) : -0.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.058 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4269 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3959 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5791 ; 1.277 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9091 ; 0.923 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 514 ; 6.230 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;32.235 ;23.260 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 695 ;13.944 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;19.446 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 618 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4778 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 989 ; 0.001 ; 0.020 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): 8222 ; 4.422 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 131 ;35.391 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 8411 ;11.133 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 245 4 REMARK 3 1 B 1 B 245 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 3767 ; 0.500 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 3767 ; 4.630 ; 2.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 C 1 C 101 5 REMARK 3 1 D 1 D 101 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 C (A): 74 ; 0.570 ; 0.500 REMARK 3 LOOSE POSITIONAL 2 C (A): 143 ; 0.720 ; 5.000 REMARK 3 MEDIUM THERMAL 2 C (A**2): 74 ; 5.640 ; 2.000 REMARK 3 LOOSE THERMAL 2 C (A**2): 143 ; 3.660 ;10.000 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4MNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.25 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 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56805 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 16% GLYCEROL, 0.17 M REMARK 280 AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.25, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.22850 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 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE BICYCLIC PEPTIDE UK903 IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BICYCLIC PEPTIDE UK903 REMARK 400 CHAIN: C REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE 29O REMARK 400 DESCRIPTION: 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 62.21 -153.47 REMARK 500 VAL A 41 -67.22 -107.01 REMARK 500 SER A 54 -159.74 -150.18 REMARK 500 ASP A 97 -152.52 -101.27 REMARK 500 LEU A 97B -58.99 -133.05 REMARK 500 TYR A 171 -104.73 -97.23 REMARK 500 SER A 214 -58.24 -122.92 REMARK 500 GLN B 27 63.44 -150.51 REMARK 500 VAL B 41 -66.50 -109.13 REMARK 500 ASP B 97 -150.51 -104.79 REMARK 500 LEU B 97B -60.91 -138.29 REMARK 500 TYR B 171 -99.79 -99.51 REMARK 500 SER B 214 -56.94 -122.24 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 SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR BICYCLIC PEPTIDE UK903 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR BICYCLIC PEPTIDE UK903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MNV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BICYCLIC PEPTIDE UK729 BOUND AS AN ACYL-ENZYME REMARK 900 INTERMEDIATE TO UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 RELATED ID: 4MNW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK749 REMARK 900 RELATED ID: 4MNX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK811 REMARK 900 RELATED ID: 3QN7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK18 REMARK 900 RELATED ID: 2NWN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH MONO-CYCLIC PEPTIDE UPAIN-1 REMARK 900 RELATED ID: 4JK5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK18-D-SER REMARK 900 RELATED ID: 4JK6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK18-D-ABA REMARK 900 RELATED ID: 4GLY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK504 DBREF 4MNY A 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4MNY B 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4MNY C 1 14 PDB 4MNY 4MNY 1 14 DBREF 4MNY D 1 14 PDB 4MNY 4MNY 1 14 SEQADV 4MNY ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4MNY GLN A 145 UNP P00749 ASN 322 ENGINEERED MUTATION SEQADV 4MNY ALA B 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4MNY GLN B 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 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 ILE 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 ALA 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 GLN 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 SEQRES 1 C 14 GLY CYS GLN VAL ASN TYR CYS PRO PRO VAL PRO CYS LEU SEQRES 2 C 14 NH2 SEQRES 1 D 14 GLY CYS GLN VAL ASN TYR CYS PRO PRO VAL PRO CYS LEU SEQRES 2 D 14 NH2 HET NH2 C 14 1 HET NH2 D 14 1 HET SO4 A1001 5 HET SO4 A1002 5 HET ACT A1003 4 HET ACT A1004 4 HET GOL A1005 6 HET GOL A1006 6 HET SO4 B 301 5 HET SO4 B 302 5 HET ACT B 303 4 HET ACT B 304 4 HET GOL B 305 6 HET ACT B 306 4 HET 29O C 101 18 HET 29O D 101 18 HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM 29O N,N',N''-BENZENE-1,3,5-TRIYLTRIS(2-BROMOACETAMIDE) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NH2 2(H2 N) FORMUL 5 SO4 4(O4 S 2-) FORMUL 7 ACT 5(C2 H3 O2 1-) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 17 29O 2(C12 H12 BR3 N3 O3) FORMUL 19 HOH *429(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 HELIX 7 7 THR B 23 GLN B 27 5 5 HELIX 8 8 ALA B 55 PHE B 59 5 5 HELIX 9 9 LYS B 61 GLU B 62A 5 3 HELIX 10 10 SER B 164 GLN B 169 1 6 HELIX 11 11 TYR B 172 VAL B 176 5 5 HELIX 12 12 PHE B 234 THR B 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 ALA A 184 N LYS A 161 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 ILE A 212 O THR A 229 SHEET 6 A 8 PRO A 198 LEU A 203 -1 N LEU A 203 O ARG A 206 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 ALA A 104 N SER A 54 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 SHEET 1 C 2 SER A 95 ALA A 96 0 SHEET 2 C 2 HIS A 99 HIS A 100 -1 O HIS A 100 N SER A 95 SHEET 1 D 8 GLU B 20 PHE B 21 0 SHEET 2 D 8 LYS B 156 ILE B 163 -1 O MET B 157 N GLU B 20 SHEET 3 D 8 MET B 180 ALA B 184 -1 O ALA B 184 N LYS B 161 SHEET 4 D 8 GLY B 226 ARG B 230 -1 O TYR B 228 N LEU B 181 SHEET 5 D 8 ARG B 206 TRP B 215 -1 N TRP B 215 O VAL B 227 SHEET 6 D 8 PRO B 198 LEU B 203 -1 N LEU B 199 O GLY B 211 SHEET 7 D 8 SER B 135 GLY B 140 -1 N GLU B 137 O VAL B 200 SHEET 8 D 8 LYS B 156 ILE B 163 -1 O VAL B 160 N CYS B 136 SHEET 1 E 7 PHE B 30 ARG B 36 0 SHEET 2 E 7 VAL B 38 SER B 48 -1 O VAL B 41 N ILE B 33 SHEET 3 E 7 TRP B 51 SER B 54 -1 O ILE B 53 N SER B 45 SHEET 4 E 7 ALA B 104 ARG B 109 -1 O LEU B 106 N VAL B 52 SHEET 5 E 7 MET B 81 LEU B 90 -1 N ILE B 89 O LEU B 105 SHEET 6 E 7 TYR B 64 LEU B 68 -1 N LEU B 68 O MET B 81 SHEET 7 E 7 PHE B 30 ARG B 36 -1 N TYR B 34 O ILE B 65 SHEET 1 F 2 SER B 95 ALA B 96 0 SHEET 2 F 2 HIS B 99 HIS B 100 -1 O HIS B 100 N SER B 95 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.03 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.04 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.05 SSBOND 6 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 7 CYS B 50 CYS B 111 1555 1555 2.04 SSBOND 8 CYS B 136 CYS B 201 1555 1555 2.04 SSBOND 9 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 10 CYS B 191 CYS B 220 1555 1555 2.05 LINK C LEU C 13 N NH2 C 14 1555 1555 1.33 LINK C LEU D 13 N NH2 D 14 1555 1555 1.33 LINK SG CYS D 7 C10 29O D 101 1555 1555 1.81 LINK SG CYS C 7 C10 29O C 101 1555 1555 1.81 LINK SG CYS C 12 C12 29O C 101 1555 1555 1.82 LINK SG CYS D 12 C12 29O D 101 1555 1555 1.83 LINK SG CYS D 2 C9 29O D 101 1555 1555 1.86 LINK SG CYS C 2 C9 29O C 101 1555 1555 1.88 SITE 1 AC1 3 HIS A 37 ARG A 37A HOH A1171 SITE 1 AC2 8 THR A 39 TYR A 40 HOH A1141 HOH A1144 SITE 2 AC2 8 HOH A1200 HOH A1222 HOH A1259 HOH A1265 SITE 1 AC3 7 VAL A 41 HIS A 57 GLN A 192 GLY A 193 SITE 2 AC3 7 SER A 195 HOH A1258 TYR C 6 SITE 1 AC4 2 ARG A 239 THR A 242 SITE 1 AC5 6 HIS A 100 ASN A 101 THR A 177 LYS A 179 SITE 2 AC5 6 MET A 180 HOH A1227 SITE 1 AC6 3 HIS A 165 ARG A 166 HOH A1317 SITE 1 AC7 2 HIS B 37 ARG B 37A SITE 1 AC8 8 THR B 39 TYR B 40 TYR B 151 ACT B 306 SITE 2 AC8 8 HOH B 470 HOH B 525 HOH B 527 HOH B 528 SITE 1 AC9 7 VAL B 41 HIS B 57 GLN B 192 GLY B 193 SITE 2 AC9 7 SER B 195 HOH B 401 TYR D 6 SITE 1 BC1 3 TYR B 67 ARG B 70 HOH B 454 SITE 1 BC2 4 HIS B 100 ASN B 101 THR B 177 LYS B 179 SITE 1 BC3 4 LEU B 73 ASN B 74 TYR B 151 SO4 B 302 SITE 1 BC4 36 HIS A 57 ASP A 60A HIS A 99 LYS A 143 SITE 2 BC4 36 SER A 146 THR A 147 ASP A 148 SER A 190 SITE 3 BC4 36 CYS A 191 GLN A 192 SER A 195 VAL A 213 SITE 4 BC4 36 SER A 214 TRP A 215 GLY A 216 ARG A 217 SITE 5 BC4 36 GLY A 218 CYS A 220 GLY A 226 ACT A1003 SITE 6 BC4 36 HOH A1106 HOH A1108 HOH A1123 HOH A1159 SITE 7 BC4 36 HOH A1160 HOH C 201 HOH C 202 HOH C 203 SITE 8 BC4 36 HOH C 204 HOH C 206 HOH C 207 HOH C 212 SITE 9 BC4 36 HOH C 214 HOH C 215 HOH C 216 HOH C 217 SITE 1 BC5 34 HIS B 57 ASP B 60A HIS B 99 LYS B 143 SITE 2 BC5 34 SER B 146 THR B 147 ASP B 148 SER B 190 SITE 3 BC5 34 CYS B 191 GLN B 192 SER B 195 VAL B 213 SITE 4 BC5 34 TRP B 215 GLY B 216 ARG B 217 GLY B 218 SITE 5 BC5 34 CYS B 220 GLY B 226 ACT B 303 HOH B 413 SITE 6 BC5 34 HOH B 427 HOH B 446 HOH D 201 HOH D 202 SITE 7 BC5 34 HOH D 203 HOH D 204 HOH D 205 HOH D 206 SITE 8 BC5 34 HOH D 207 HOH D 209 HOH D 210 HOH D 213 SITE 9 BC5 34 HOH D 221 HOH D 222 CRYST1 67.959 54.457 71.681 90.00 98.18 90.00 P 1 21 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 0.014715 0.000000 0.002114 0.00000 SCALE2 0.000000 0.018363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014094 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.951320 -0.004525 0.308173 15.57428 1 MTRIX2 2 -0.002480 -0.999972 -0.007029 -19.42945 1 MTRIX3 2 0.308196 0.005923 -0.951304 -95.49374 1