HEADER HYDROLASE/HYDROLASE INHIBITOR 11-SEP-13 4MNX TITLE CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) TITLE 2 COMPLEXED WITH BICYCLIC PEPTIDE UK811 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 3 CHAIN: A; 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 UK811; COMPND 11 CHAIN: B; 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 1,3,5-TRIACRYLOYL-1,3,5-TRIAZINANE SOURCE 15 (TATA) KEYWDS COMPETITIVE INHIBITOR, BICYCLIC PEPTIDE, INHIBITOR, PROTEASE, 1, 1', KEYWDS 2 1''-(1, 3, 5-TRIAZINANE-1, 5-TRIYL)TRIPROP-2-EN-1-ONE (TATA) KEYWDS 3 CYCLIZATION, EXTRACELLULAR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,F.POJER,C.HEINIS REVDAT 3 15-NOV-17 4MNX 1 REMARK REVDAT 2 26-FEB-14 4MNX 1 JRNL REVDAT 1 05-FEB-14 4MNX 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 18289 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1298 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2041 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : -2.16000 REMARK 3 B33 (A**2) : 1.85000 REMARK 3 B12 (A**2) : 0.00000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.822 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2130 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1977 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2888 ; 1.370 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4542 ; 0.777 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 6.632 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;34.929 ;23.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;15.388 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;12.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2378 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 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): 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 : 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 4MNX 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_1000082147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 44.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.62100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 35.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG4000, 15% GLYCEROL, 0.17 M REMARK 280 AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 26.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 REMARK 400 THE BICYCLIC PEPTIDE UK811 IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BICYCLIC PEPTIDE UK811 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE 29N 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 VAL A 41 -66.77 -109.42 REMARK 500 SER A 54 -154.34 -148.97 REMARK 500 PRO A 60C 36.35 -79.55 REMARK 500 TYR A 171 -104.15 -95.32 REMARK 500 SER A 214 -61.08 -121.32 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 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 GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR BICYCLIC PEPTIDE UK811 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: 4MNY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK903 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 4MNX A 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4MNX B 1 14 PDB 4MNX 4MNX 1 14 SEQADV 4MNX ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4MNX 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 LEU CYS SER ASP ARG GLY CYS GLU ASN ARG TRP CYS LYS SEQRES 2 B 14 NH2 HET NH2 B 14 1 HET SO4 A 301 5 HET SO4 A 302 5 HET GOL A 303 6 HET 29N B 101 18 HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM 29N 1,1',1''-(1,3,5-TRIAZINANE-1,3,5-TRIYL)TRIPROPAN-1-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 29N 1,1',1''-(1,3,5-TRIAZINANE-1,3,5-TRIYL)TRIPROP-2-EN-1- HETSYN 2 29N ONE, BOUND FORM FORMUL 2 NH2 H2 N FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 29N C12 H21 N3 O3 FORMUL 7 HOH *128(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 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 THR A 39 N ARG A 35 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 LEU A 68 O MET A 81 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 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.04 SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.00 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.00 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.02 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.03 LINK C LYS B 13 N NH2 B 14 1555 1555 1.32 LINK SG CYS B 12 C16 29N B 101 1555 1555 1.83 LINK SG CYS B 7 C25 29N B 101 1555 1555 1.84 LINK SG CYS B 2 C19 29N B 101 1555 1555 1.84 SITE 1 AC1 7 LYS A 61 HIS A 100 THR A 177 LYS A 179 SITE 2 AC1 7 MET A 180 HOH A 432 HOH A 461 SITE 1 AC2 5 PHE A 132 SER A 164 HIS A 165 ARG A 166 SITE 2 AC2 5 ARG A 206 SITE 1 AC3 5 ARG A 35 HIS A 37 ARG A 37A HOH A 509 SITE 2 AC3 5 HOH A 513 SITE 1 AC4 43 GLY A 18 GLY A 19 GLU A 20 PHE A 21 SITE 2 AC4 43 ASN A 26 ARG A 35 VAL A 41 CYS A 42 SITE 3 AC4 43 HIS A 57 CYS A 58 ASP A 60A TYR A 60B SITE 4 AC4 43 TYR A 64 THR A 97A LEU A 97B GLU A 144 SITE 5 AC4 43 GLN A 145 ASP A 148 LYS A 156 ASP A 189 SITE 6 AC4 43 SER A 190 CYS A 191 GLN A 192 GLY A 193 SITE 7 AC4 43 SER A 195 SER A 214 TRP A 215 GLY A 216 SITE 8 AC4 43 GLY A 218 GLY A 226 HOH A 420 HOH A 430 SITE 9 AC4 43 HOH A 434 HOH A 435 HOH A 466 HOH B 201 SITE 10 AC4 43 HOH B 202 HOH B 203 HOH B 204 HOH B 205 SITE 11 AC4 43 HOH B 206 HOH B 208 HOH B 209 CRYST1 52.450 53.500 79.580 90.00 90.00 90.00 P 21 21 21 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 0.019066 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012566 0.00000