HEADER HYDROLASE/HYDROLASE INHIBITOR 09-MAR-13 4JK6 TITLE HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) IN COMPLEX WITH A TITLE 2 BICYCLIC PEPTIDE INHIBITOR (UK18-D-ABA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; 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 UK18-D-ABA INHIBITOR OF UPA; 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_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK-293; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PSECTAGA; SOURCE 13 MOL_ID: 2; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS SERINE PROTEASE, CHYMOTRYPSIN FOLD, UROKINASE-TYPE PLASMINOGEN KEYWDS 2 ACTIVATOR, BICYCLIC PEPTIDE INHIBITOR, D-AMINO ACIDS, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.A.BUTH,P.G.LEIMAN,S.CHEN,C.HEINIS REVDAT 5 06-DEC-23 4JK6 1 LINK REVDAT 4 20-SEP-23 4JK6 1 SOURCE REMARK SEQADV LINK REVDAT 3 15-NOV-17 4JK6 1 REMARK REVDAT 2 31-JUL-13 4JK6 1 JRNL REVDAT 1 17-JUL-13 4JK6 0 JRNL AUTH S.CHEN,D.GFELLER,S.A.BUTH,O.MICHIELIN,P.G.LEIMAN,C.HEINIS JRNL TITL IMPROVING BINDING AFFINITY AND STABILITY OF PEPTIDE LIGANDS JRNL TITL 2 BY SUBSTITUTING GLYCINES WITH D-AMINO ACIDS. JRNL REF CHEMBIOCHEM V. 14 1316 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23828687 JRNL DOI 10.1002/CBIC.201300228 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11311 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) : 0.153 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 564 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 853 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : 1.54000 REMARK 3 B12 (A**2) : -0.47000 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): 0.333 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.095 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2176 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2004 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2949 ; 1.845 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4611 ; 0.851 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 7.373 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;31.345 ;22.979 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 358 ;16.461 ;15.014 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.272 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 313 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2426 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 505 ; 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 : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): -35.4980 113.3080 -2.4820 REMARK 3 T TENSOR REMARK 3 T11: 0.1526 T22: 0.1516 REMARK 3 T33: 0.0895 T12: 0.0275 REMARK 3 T13: -0.0128 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 2.9957 L22: 3.8360 REMARK 3 L33: 1.4802 L12: -0.9588 REMARK 3 L13: -0.1446 L23: -0.0676 REMARK 3 S TENSOR REMARK 3 S11: -0.0872 S12: -0.0374 S13: -0.0862 REMARK 3 S21: -0.0220 S22: 0.0948 S23: 0.3783 REMARK 3 S31: 0.1443 S32: -0.2303 S33: -0.0077 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 78 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): -35.5840 106.1310 5.6040 REMARK 3 T TENSOR REMARK 3 T11: 0.2045 T22: 0.1848 REMARK 3 T33: 0.0868 T12: 0.0067 REMARK 3 T13: 0.0325 T23: 0.0675 REMARK 3 L TENSOR REMARK 3 L11: 24.1100 L22: 20.9184 REMARK 3 L33: 7.0205 L12: -16.8935 REMARK 3 L13: -5.5735 L23: 6.2812 REMARK 3 S TENSOR REMARK 3 S11: -0.2953 S12: -0.3570 S13: -0.4826 REMARK 3 S21: 0.6736 S22: 0.2784 S23: 0.1894 REMARK 3 S31: 0.4967 S32: -0.1348 S33: 0.0170 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 85 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): -37.1550 121.0620 2.7730 REMARK 3 T TENSOR REMARK 3 T11: 0.1218 T22: 0.1847 REMARK 3 T33: 0.1752 T12: 0.0776 REMARK 3 T13: 0.0204 T23: -0.0316 REMARK 3 L TENSOR REMARK 3 L11: 6.3380 L22: 5.0728 REMARK 3 L33: 1.8410 L12: -1.2187 REMARK 3 L13: 0.6700 L23: -0.5233 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: -0.4909 S13: 0.5077 REMARK 3 S21: 0.3848 S22: 0.2575 S23: 0.3985 REMARK 3 S31: -0.1425 S32: -0.4536 S33: -0.1945 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 124 A 128 REMARK 3 ORIGIN FOR THE GROUP (A): -24.8970 135.7580 5.1760 REMARK 3 T TENSOR REMARK 3 T11: 0.4821 T22: 0.1664 REMARK 3 T33: 0.7563 T12: 0.0799 REMARK 3 T13: -0.2208 T23: -0.3108 REMARK 3 L TENSOR REMARK 3 L11: 4.0544 L22: 17.3163 REMARK 3 L33: 24.2366 L12: -5.5454 REMARK 3 L13: -2.0456 L23: -10.2744 REMARK 3 S TENSOR REMARK 3 S11: -0.6777 S12: -0.3027 S13: 0.3589 REMARK 3 S21: 1.3827 S22: 0.4310 S23: 0.4279 REMARK 3 S31: -1.4087 S32: -0.4855 S33: 0.2467 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 129 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): -25.0760 116.9190 -10.7610 REMARK 3 T TENSOR REMARK 3 T11: 0.2009 T22: 0.1302 REMARK 3 T33: 0.1341 T12: 0.0768 REMARK 3 T13: 0.0220 T23: 0.0245 REMARK 3 L TENSOR REMARK 3 L11: 2.8841 L22: 3.3965 REMARK 3 L33: 1.5932 L12: 0.1740 REMARK 3 L13: -0.6298 L23: -0.0488 REMARK 3 S TENSOR REMARK 3 S11: 0.0962 S12: 0.1934 S13: 0.4202 REMARK 3 S21: -0.3371 S22: -0.1934 S23: -0.2379 REMARK 3 S31: -0.1064 S32: 0.1413 S33: 0.0972 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 157 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3310 132.5000 -12.8090 REMARK 3 T TENSOR REMARK 3 T11: 0.1787 T22: 0.1531 REMARK 3 T33: 0.8380 T12: 0.0170 REMARK 3 T13: 0.0750 T23: 0.2325 REMARK 3 L TENSOR REMARK 3 L11: 1.6502 L22: 12.4373 REMARK 3 L33: 4.3071 L12: 3.0388 REMARK 3 L13: -0.3151 L23: -1.9143 REMARK 3 S TENSOR REMARK 3 S11: -0.0353 S12: 0.3204 S13: 0.9678 REMARK 3 S21: -0.1287 S22: 0.3602 S23: 0.5283 REMARK 3 S31: -0.8123 S32: -0.1763 S33: -0.3249 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 171 A 206 REMARK 3 ORIGIN FOR THE GROUP (A): -24.1240 127.4940 -9.4850 REMARK 3 T TENSOR REMARK 3 T11: 0.1784 T22: 0.1096 REMARK 3 T33: 0.3581 T12: 0.0123 REMARK 3 T13: 0.0595 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 4.3436 L22: 3.2500 REMARK 3 L33: 1.2831 L12: 0.6604 REMARK 3 L13: -0.1234 L23: -0.2165 REMARK 3 S TENSOR REMARK 3 S11: 0.0608 S12: 0.0269 S13: 0.9838 REMARK 3 S21: -0.1855 S22: 0.0542 S23: -0.3951 REMARK 3 S31: -0.3270 S32: 0.1108 S33: -0.1149 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 207 A 237 REMARK 3 ORIGIN FOR THE GROUP (A): -28.2040 128.9880 -7.3580 REMARK 3 T TENSOR REMARK 3 T11: 0.1971 T22: 0.1320 REMARK 3 T33: 0.4673 T12: 0.0450 REMARK 3 T13: 0.0117 T23: 0.0294 REMARK 3 L TENSOR REMARK 3 L11: 3.3194 L22: 2.3844 REMARK 3 L33: 1.9511 L12: -0.4183 REMARK 3 L13: -0.5284 L23: 0.0592 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: 0.0826 S13: 0.9659 REMARK 3 S21: -0.1995 S22: 0.1050 S23: -0.2677 REMARK 3 S31: -0.2657 S32: 0.0318 S33: -0.2282 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 238 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): -37.7790 130.0270 9.8230 REMARK 3 T TENSOR REMARK 3 T11: 0.4439 T22: 0.7695 REMARK 3 T33: 0.4958 T12: 0.1295 REMARK 3 T13: -0.1504 T23: -0.4596 REMARK 3 L TENSOR REMARK 3 L11: 1.8704 L22: 39.9106 REMARK 3 L33: 11.4920 L12: 2.8037 REMARK 3 L13: -1.7888 L23: 15.8712 REMARK 3 S TENSOR REMARK 3 S11: 0.4993 S12: -0.5836 S13: -0.0619 REMARK 3 S21: 2.3632 S22: -0.5567 S23: -0.5562 REMARK 3 S31: 0.2339 S32: 0.4357 S33: 0.0575 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 4JK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078148. 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 : 4.9 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 : MIRRORS 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 : 11879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 33.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : 0.30800 REMARK 200 FOR SHELL : 3.700 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: PDB ENTRY 2NWN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM NA3(CIT) PH 4.9, 5% V/V PEG400, REMARK 280 1.8M (NH4)2SO4, 0.05% NAN3, 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 60.60950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.99291 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.24367 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.60950 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 34.99291 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.24367 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.60950 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 34.99291 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.24367 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.98582 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.48733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.98582 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.48733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.98582 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 28.48733 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: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 UK18-D-ABA INHIBITOR OF UPA IS CYCLIC PEPTIDE, REMARK 400 A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BICYCLIC PEPTIDE UK18-D-ABA INHIBITOR OF UPA 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: 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 OH TYR A 149 O HOH A 427 2.11 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. = -3.7 DEGREES REMARK 500 ASN A 87 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 CYS B 2 CA - CB - SG ANGL. DEV. = 11.9 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 ARG A 37A -38.91 -34.53 REMARK 500 SER A 54 -156.61 -156.04 REMARK 500 ASP A 97 -164.42 -67.34 REMARK 500 LEU A 97B -57.07 -125.56 REMARK 500 GLN A 169 34.18 -91.08 REMARK 500 TYR A 171 -109.13 -97.54 REMARK 500 SER A 214 -60.16 -122.51 REMARK 500 SER B 3 -164.86 -110.60 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 SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 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 RESIDUE P6G A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE REMARK 800 UK18-D-ABA INHIBITOR OF UPA 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 BRIGE PEPTIDE UK504 REMARK 900 RELATED ID: 3QN7 RELATED DB: PDB REMARK 900 HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) IN COMPLEX WITH A REMARK 900 BICYCLIC PEPTIDE INHIBITOR (UK18) DBREF 4JK6 A 16 242 UNP P00749 UROK_HUMAN 179 423 DBREF 4JK6 B 1 18 PDB 4JK6 4JK6 1 18 SEQADV 4JK6 ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4JK6 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 18 ALA CYS SER ARG TYR GLU VAL ASP CYS ARG GLY ARG DBB SEQRES 2 B 18 SER ALA CYS GLY NH2 HET DBB B 13 6 HET NH2 B 18 1 HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET CL A 305 1 HET P6G A 306 19 HET ZBR B 101 9 HETNAM DBB D-ALPHA-AMINOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM P6G HEXAETHYLENE GLYCOL HETNAM ZBR 1,3,5-TRIS(BROMOMETHYL)BENZENE HETSYN P6G POLYETHYLENE GLYCOL PEG400 FORMUL 2 DBB C4 H9 N O2 FORMUL 2 NH2 H2 N FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 CL CL 1- FORMUL 8 P6G C12 H26 O7 FORMUL 9 ZBR C9 H9 BR3 FORMUL 10 HOH *110(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 MET A 207 TRP A 215 -1 N ILE A 212 O THR A 229 SHEET 6 A 8 PRO A 198 SER A 202 -1 N CYS A 201 O THR A 208 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 2.08 SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.04 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.06 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.05 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.14 LINK SG CYS B 2 C8 ZBR B 101 1555 1555 1.84 LINK SG CYS B 9 C7 ZBR B 101 1555 1555 1.88 LINK C ARG B 12 N DBB B 13 1555 1555 1.32 LINK C DBB B 13 N SER B 14 1555 1555 1.33 LINK SG CYS B 16 C9 ZBR B 101 1555 1555 1.84 LINK C GLY B 17 N NH2 B 18 1555 1555 1.33 SITE 1 AC1 3 HIS A 37 ARG A 37A TYR B 5 SITE 1 AC2 5 SER A 75 ASN A 76 ARG A 206 HOH A 450 SITE 2 AC2 5 HOH A 455 SITE 1 AC3 6 PHE A 21 THR A 23 SER A 115 ARG A 116 SITE 2 AC3 6 HOH A 430 HOH A 470 SITE 1 AC4 6 LYS A 62 LEU A 88 GLN A 170 PRO A 170A SITE 2 AC4 6 HIS A 170B HOH A 469 SITE 1 AC5 4 LEU A 90 HIS A 91 LYS A 92 TRP A 237 SITE 1 AC6 4 ASN A 74 LEU A 150 SER A 202 HOH A 436 SITE 1 AC7 33 ARG A 35 HIS A 37 SER A 37D THR A 39 SITE 2 AC7 33 TYR A 40 VAL A 41 CYS A 42 HIS A 57 SITE 3 AC7 33 ILE A 60 ASP A 60A TYR A 60B HIS A 99 SITE 4 AC7 33 TYR A 127 TYR A 151 ARG A 166 THR A 178 SITE 5 AC7 33 ASP A 189 SER A 190 GLN A 192 GLY A 193 SITE 6 AC7 33 SER A 195 GLY A 216 GLY A 218 CYS A 220 SITE 7 AC7 33 GLY A 226 SO4 A 301 HOH A 444 HOH A 466 SITE 8 AC7 33 HOH A 475 HOH B 201 HOH B 202 HOH B 203 SITE 9 AC7 33 HOH B 205 CRYST1 121.219 121.219 42.731 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 0.008250 0.004763 0.000000 0.00000 SCALE2 0.000000 0.009526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023402 0.00000