HEADER HYDROLASE/HYDROLASE INHIBITOR 11-SEP-13 4MNW
TITLE CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA)
TITLE 2 COMPLEXED WITH BICYCLIC PEPTIDE UK749
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 UK749;
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-TRIS(BROMOMETHYL)BENZENE (TBMB)
KEYWDS COMPETITIVE INHIBITOR, BICYCLIC PEPTIDE, INHIBITOR, PROTEASE, 1, 3,
KEYWDS 2 5-TRIS(BROMOMETHYL)BENZENE (TBMB) CYCLIZATION, EXTRACELLULAR,
KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.CHEN,F.POJER,C.HEINIS
REVDAT 3 15-NOV-17 4MNW 1 REMARK
REVDAT 2 26-FEB-14 4MNW 1 JRNL
REVDAT 1 05-FEB-14 4MNW 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. 1.49 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) : 1.49
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.96
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 3 NUMBER OF REFLECTIONS : 34787
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) : 0.156
REMARK 3 R VALUE (WORKING SET) : 0.155
REMARK 3 FREE R VALUE : 0.171
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1811
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) : 1.49
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2597
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.09
REMARK 3 BIN R VALUE (WORKING SET) : 0.1490
REMARK 3 BIN FREE R VALUE SET COUNT : 126
REMARK 3 BIN FREE R VALUE : 0.1750
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2044
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 53
REMARK 3 SOLVENT ATOMS : 169
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.84
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.03000
REMARK 3 B22 (A**2) : 1.71000
REMARK 3 B33 (A**2) : -1.67000
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): 0.094
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.140
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2153 ; 0.005 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1990 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2913 ; 1.164 ; 1.962
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4573 ; 1.904 ; 3.006
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 6.059 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;35.569 ;23.333
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 357 ;12.115 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;11.187 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.070 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2398 ; 0.004 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 504 ; 0.002 ; 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): 4143 ; 5.010 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 52 ;26.885 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4209 ; 7.761 ; 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 ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 4MNW 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_1000082146.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-DEC-12
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 : 36626
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490
REMARK 200 RESOLUTION RANGE LOW (A) : 44.760
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.13200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 0.18300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.700
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 (%): 36.83
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95
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 26.28500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.08500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.98000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.08500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.28500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.98000
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: 3160 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11850 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 UK749 IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR
REMARK 400 CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: BICYCLIC PEPTIDE UK749
REMARK 400 CHAIN: B
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 COMPONENT_2: RESIDUE ZBR
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 -64.49 -106.26
REMARK 500 SER A 54 -156.90 -149.45
REMARK 500 PRO A 60C 44.18 -84.81
REMARK 500 ASP A 93 34.34 -98.16
REMARK 500 TYR A 171 -110.99 -90.97
REMARK 500 SER A 214 -56.94 -124.55
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 GOL A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 308
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR BICYCLIC PEPTIDE UK749
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: 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: 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 4MNW A 16 242 UNP P00749 UROK_HUMAN 179 423
DBREF 4MNW B 1 14 PDB 4MNW 4MNW 1 14
SEQADV 4MNW ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION
SEQADV 4MNW 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 GLN CYS TRP ASP ARG GLY CYS GLU ASN ARG LYS CYS ASN
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 GOL A 304 6
HET GOL A 305 6
HET GOL A 306 6
HET GOL A 307 6
HET ACT A 308 4
HET ZBR B 101 9
HETNAM NH2 AMINO GROUP
HETNAM SO4 SULFATE ION
HETNAM GOL GLYCEROL
HETNAM ACT ACETATE ION
HETNAM ZBR 1,3,5-TRIS(BROMOMETHYL)BENZENE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 NH2 H2 N
FORMUL 3 SO4 2(O4 S 2-)
FORMUL 5 GOL 5(C3 H8 O3)
FORMUL 10 ACT C2 H3 O2 1-
FORMUL 11 ZBR C9 H9 BR3
FORMUL 12 HOH *169(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 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
SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.02
SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.03
SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.03
SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.04
SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.05
LINK C ASN B 13 N NH2 B 14 1555 1555 1.33
LINK SG CYS B 12 C7 ZBR B 101 1555 1555 1.82
LINK SG CYS B 2 C8 ZBR B 101 1555 1555 1.82
LINK SG CYS B 7 C9 ZBR B 101 1555 1555 1.84
SITE 1 AC1 8 LYS A 61 HIS A 100 THR A 177 LYS A 179
SITE 2 AC1 8 MET A 180 GOL A 306 HOH A 518 HOH A 550
SITE 1 AC2 5 SER A 164 HIS A 165 ARG A 166 ARG A 206
SITE 2 AC2 5 HOH A 549
SITE 1 AC3 9 THR A 23 SER A 71 ARG A 72 THR A 77
SITE 2 AC3 9 GLN A 154 HOH A 523 GLN B 1 CYS B 2
SITE 3 AC3 9 TRP B 3
SITE 1 AC4 6 HIS A 165 GLN A 169 THR A 177 THR A 178
SITE 2 AC4 6 HOH A 518 HOH A 550
SITE 1 AC5 4 ARG A 35 HIS A 37 ARG A 37A LYS A 187
SITE 1 AC6 10 HIS A 99 HIS A 100 ASN A 101 ASP A 102
SITE 2 AC6 10 LYS A 179 MET A 180 SER A 214 TRP A 215
SITE 3 AC6 10 THR A 229 SO4 A 301
SITE 1 AC7 4 TRP A 186 LYS A 187 ALA A 221 HOH A 515
SITE 1 AC8 3 SER A 125 MET A 126 ARG A 239
SITE 1 AC9 44 GLU A 20 PHE A 21 THR A 22 THR A 23
SITE 2 AC9 44 ARG A 35 VAL A 41 HIS A 57 CYS A 58
SITE 3 AC9 44 ASP A 60A TYR A 60B TYR A 64 ARG A 72
SITE 4 AC9 44 LEU A 97B HIS A 99 GLU A 144 GLN A 154
SITE 5 AC9 44 GLN A 169 SER A 174 ASP A 189 SER A 190
SITE 6 AC9 44 GLN A 192 GLY A 193 SER A 195 TRP A 215
SITE 7 AC9 44 GLY A 216 ARG A 217 GLY A 218 LYS A 224
SITE 8 AC9 44 GLY A 226 GOL A 303 HOH A 404 HOH A 442
SITE 9 AC9 44 HOH A 466 HOH A 526 HOH A 530 HOH B 201
SITE 10 AC9 44 HOH B 202 HOH B 203 HOH B 204 HOH B 205
SITE 11 AC9 44 HOH B 206 HOH B 207 HOH B 208 HOH B 209
CRYST1 52.570 53.960 80.170 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 0.019022 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018532 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012474 0.00000
(ATOM LINES ARE NOT SHOWN.)
END