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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
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