HEADER HYDROLASE/HYDROLASE INHIBITOR 12-FEB-14 4OS4 TITLE CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) TITLE 2 COMPLEXED WITH BICYCLIC PEPTIDE UK603 (BICYCLIC 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 179-423); 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 UK603 (BICYCLIC 1); 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 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: HEK293; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSECTAGA; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES KEYWDS BICYCLIC PEPTIDE, INHIBITOR, PROTEASE, DISULFIDE BRIDGES, KEYWDS 2 CYCLIZATION, EXTRACELLULAR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,F.POJER,C.HEINIS REVDAT 4 02-JUN-21 4OS4 1 SOURCE REMARK SEQADV LINK REVDAT 3 22-NOV-17 4OS4 1 REMARK REVDAT 2 05-NOV-14 4OS4 1 JRNL REVDAT 1 24-SEP-14 4OS4 0 JRNL AUTH S.CHEN,R.GOPALAKRISHNAN,T.SCHAER,F.MARGER,R.HOVIUS, JRNL AUTH 2 D.BERTRAND,F.POJER,C.HEINIS JRNL TITL DITHIOL AMINO ACIDS CAN STRUCTURALLY SHAPE AND ENHANCE THE JRNL TITL 2 LIGAND-BINDING PROPERTIES OF POLYPEPTIDES. JRNL REF NAT CHEM V. 6 1009 2014 JRNL REFN ESSN 1755-4349 JRNL PMID 25343607 JRNL DOI 10.1038/NCHEM.2043 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 15344 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 960 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1109 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.1510 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.2010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : 1.27000 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): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.333 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2110 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1963 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2858 ; 1.291 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4511 ; 0.753 ; 3.016 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.261 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;31.587 ;23.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 351 ;15.724 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.251 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 307 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2363 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 496 ; 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 4OS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-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 : 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16342 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.05000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 21.80 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% 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 26.21350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.49400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.93700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.49400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.21350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.93700 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: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 UK603 (BICYCLIC 1) IS CYCLIC PEPTIDE, A MEMBER REMARK 400 OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BICYCLIC PEPTIDE UK603 (BICYCLIC 1) 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: 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 51.91 -142.68 REMARK 500 VAL A 41 -60.95 -107.76 REMARK 500 SER A 54 -156.63 -152.31 REMARK 500 PRO A 60C 38.63 -84.04 REMARK 500 TYR A 127 19.74 52.16 REMARK 500 TYR A 171 -107.28 -89.64 REMARK 500 SER A 214 -60.19 -124.51 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 RESIDUE ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE REMARK 800 UK603 (BICYCLIC 1) REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GLY RELATED DB: PDB REMARK 900 HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR UPA IN COMPLEX WITH THE REMARK 900 TWO-DISULFIDE BRIDGE PEPTIDE UK504 REMARK 900 RELATED ID: 4OS1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK601 (BICYCLIC 1) REMARK 900 RELATED ID: 4OS2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK602 (BICYCLIC 1) REMARK 900 RELATED ID: 4OS5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK603 (BICYCLIC 2) REMARK 900 RELATED ID: 4OS6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK604 (BICYCLIC 2) REMARK 900 RELATED ID: 4OS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) REMARK 900 COMPLEXED WITH BICYCLIC PEPTIDE UK607 (BICYCLIC) DBREF 4OS4 A 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4OS4 B 1 15 PDB 4OS4 4OS4 1 15 SEQADV 4OS4 ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4OS4 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 15 GLY 81R ALA LEU GLY ARG GLY CYS GLU ASN HIS ARG CYS SEQRES 2 B 15 LEU NH2 HET 81R B 2 9 HET NH2 B 15 1 HET SO4 A 301 5 HET SO4 A 302 5 HET GOL A 303 6 HET ACT A 304 4 HET CL A 305 1 HETNAM 81R (4R)-4,5-DISULFANYL-L-NORVALINE HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 81R C5 H11 N O2 S2 FORMUL 2 NH2 H2 N FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 CL CL 1- FORMUL 8 HOH *197(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 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 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 1.99 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.01 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.04 LINK C GLY B 1 N 81R B 2 1555 1555 1.33 LINK C 81R B 2 N ALA B 3 1555 1555 1.33 LINK SE 81R B 2 SG CYS B 8 1555 1555 2.06 LINK SD2 81R B 2 SG CYS B 13 1555 1555 2.04 LINK C LEU B 14 N NH2 B 15 1555 1555 1.36 SITE 1 AC1 6 LYS A 61 HIS A 100 THR A 177 LYS A 179 SITE 2 AC1 6 MET A 180 HOH A 402 SITE 1 AC2 3 ARG A 35 HIS A 37 ARG A 37A SITE 1 AC3 5 SER A 164 HIS A 165 ARG A 166 ARG A 206 SITE 2 AC3 5 HOH A 567 SITE 1 AC4 3 LYS A 110A LYS A 223 HOH A 461 SITE 1 AC5 3 TYR A 127 ARG A 230 HIS A 233 SITE 1 AC6 41 GLY A 19 GLU A 20 PHE A 21 THR A 22 SITE 2 AC6 41 ASN A 26 ARG A 35 VAL A 41 HIS A 57 SITE 3 AC6 41 CYS A 58 ASP A 60A TYR A 60B TYR A 64 SITE 4 AC6 41 HIS A 99 GLU A 144 SER A 174 ASP A 189 SITE 5 AC6 41 SER A 190 CYS A 191 GLN A 192 GLY A 193 SITE 6 AC6 41 SER A 195 SER A 214 TRP A 215 GLY A 218 SITE 7 AC6 41 GLY A 226 HOH A 430 HOH A 462 HOH A 475 SITE 8 AC6 41 HOH A 503 HOH A 505 HOH A 557 HOH A 561 SITE 9 AC6 41 HOH B 101 HOH B 102 HOH B 103 HOH B 104 SITE 10 AC6 41 HOH B 105 HOH B 106 HOH B 109 HOH B 110 SITE 11 AC6 41 HOH B 111 CRYST1 52.427 53.874 82.988 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 0.019074 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012050 0.00000