PDB Short entry for 3BT1 HEADER IMMUNE SYSTEM 27-DEC-07 3BT1 TITLE STRUCTURE OF UROKINASE RECEPTOR, UROKINASE AND VITRONECTIN COMPLEX CAVEAT 3BT1 NAG C 1 HAS WRONG CHIRALITY AT ATOM C1 NAG U 1172 HAS WRONG CAVEAT 2 3BT1 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UROKINASE AMINO TERMINAL FRAGMENT, UROKINASE-TYPE COMPND 5 PLASMINOGEN ACTIVATOR LONG CHAIN A, UNP RESIDUES 21-153; COMPND 6 SYNONYM: UPA, U-PLASMINOGEN ACTIVATOR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VITRONECTIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: SOMETOMEDIN-B DOMAIN; COMPND 12 SYNONYM: SERUM-SPREADING FACTOR, S-PROTEIN, V75; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR; COMPND 16 CHAIN: U; COMPND 17 SYNONYM: UPAR, U-PAR, MONOCYTE ACTIVATION ANTIGEN MO3, CD87 ANTIGEN; COMPND 18 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: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: S2 CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMT/BIP; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: VTN; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: PLAUR, MO3, UPAR; SOURCE 26 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 27 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 29 EXPRESSION_SYSTEM_STRAIN: S2 CELLS; SOURCE 30 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 31 EXPRESSION_SYSTEM_PLASMID: PMT/BIP KEYWDS PROTEIN-PROTEIN COMPLEX, GLYCOPROTEIN, GPI-ANCHOR, LIPOPROTEIN, KEYWDS 2 MEMBRANE, RECEPTOR, SECRETED, BLOOD COAGULATION, EGF-LIKE DOMAIN, KEYWDS 3 FIBRINOLYSIS, HYDROLASE, KRINGLE, PHOSPHOPROTEIN, PLASMINOGEN KEYWDS 4 ACTIVATION, PROTEASE, SERINE PROTEASE, ZYMOGEN, CELL ADHESION, KEYWDS 5 HEPARIN-BINDING, SULFATION, IMMUNOGLOBULIN DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.HUANG REVDAT 8 01-NOV-23 3BT1 1 HETSYN REVDAT 7 29-JUL-20 3BT1 1 CAVEAT COMPND REMARK HETNAM REVDAT 7 2 1 LINK SITE ATOM REVDAT 6 18-DEC-19 3BT1 1 REMARK REVDAT 5 11-DEC-19 3BT1 1 CAVEAT REMARK SEQADV SSBOND REVDAT 5 2 1 LINK REVDAT 4 13-JUL-11 3BT1 1 VERSN REVDAT 3 24-FEB-09 3BT1 1 VERSN REVDAT 2 22-APR-08 3BT1 1 JRNL REVDAT 1 25-MAR-08 3BT1 0 JRNL AUTH Q.HUAI,A.ZHOU,L.LIN,A.P.MAZAR,G.C.PARRY,J.CALLAHAN,D.E.SHAW, JRNL AUTH 2 B.FURIE,B.C.FURIE,M.HUANG JRNL TITL CRYSTAL STRUCTURES OF TWO HUMAN VITRONECTIN, UROKINASE AND JRNL TITL 2 UROKINASE RECEPTOR COMPLEXES JRNL REF NAT.STRUCT.MOL.BIOL. V. 15 422 2008 JRNL REFN ISSN 1545-9993 JRNL PMID 18376415 JRNL DOI 10.1038/NSMB.1404 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13778 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) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 726 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1005 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3990 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.5980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3394 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : -3.25000 REMARK 3 B33 (A**2) : 2.77000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.439 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.374 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 43.465 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3560 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2473 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4821 ; 1.821 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5921 ; 1.048 ; 3.016 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 9.464 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;36.371 ;24.302 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 595 ;21.248 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;19.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 510 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3950 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 686 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1061 ; 0.266 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2877 ; 0.221 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1752 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2006 ; 0.100 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.196 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.163 ; 0.200 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): 17 ; 0.185 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.246 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.064 ; 0.200 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): 2697 ; 0.746 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 909 ; 0.105 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3478 ; 0.958 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1573 ; 1.356 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1343 ; 2.154 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.05 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 3BT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.80300 REMARK 200 R SYM FOR SHELL (I) : 0.80300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2FD6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3350, 50MM HEPES PH 7.5, REMARK 280 MICRODIALYSIS, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 48.67650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.59350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.67650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.59350 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, U, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 HIS A 5 REMARK 465 GLN A 6 REMARK 465 VAL A 7 REMARK 465 ASP A 133 REMARK 465 ARG U -1 REMARK 465 SER U 0 REMARK 465 ARG U 83 REMARK 465 ALA U 84 REMARK 465 LEU U 276 REMARK 465 ASP U 277 REMARK 465 VAL U 278 REMARK 465 GLN U 279 REMARK 465 TYR U 280 REMARK 465 ARG U 281 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 ND2 ASN U 52 O5 NAG U 1052 1.68 REMARK 500 SG CYS U 3 SG CYS U 17 2.11 REMARK 500 SG CYS B 5 SG CYS B 32 2.13 REMARK 500 O THR U 54 O LEU U 66 2.13 REMARK 500 O LEU U 1 N CYS U 17 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU U 33 CB GLU U 33 CG 0.114 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 LEU U 144 CA - CB - CG ANGL. DEV. = 14.4 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 CYS A 11 167.92 69.08 REMARK 500 ASP A 12 42.10 -94.37 REMARK 500 ASN A 27 32.15 39.56 REMARK 500 LYS A 35 -110.11 57.64 REMARK 500 ASN A 54 -63.35 84.43 REMARK 500 ARG A 59 -144.84 -108.14 REMARK 500 ALA A 62 116.50 118.00 REMARK 500 ASP A 65 -159.94 -90.74 REMARK 500 ARG A 88 49.50 -157.12 REMARK 500 SER A 89 -88.98 46.39 REMARK 500 ASP A 90 -1.71 -57.06 REMARK 500 ASN A 107 54.00 36.37 REMARK 500 LEU A 119 -106.09 -90.16 REMARK 500 LYS A 120 112.22 -15.37 REMARK 500 MET A 127 75.19 -43.29 REMARK 500 GLU B 3 -112.16 -105.76 REMARK 500 SER B 4 124.42 55.68 REMARK 500 ARG B 8 -61.25 62.75 REMARK 500 CYS B 9 -7.45 80.47 REMARK 500 THR B 10 56.91 -154.52 REMARK 500 LYS B 18 -108.97 -67.39 REMARK 500 CYS B 39 70.63 -118.12 REMARK 500 LYS B 40 47.34 176.93 REMARK 500 GLU U 16 98.47 -64.72 REMARK 500 CYS U 17 56.48 -54.25 REMARK 500 ALA U 18 -163.95 77.85 REMARK 500 LEU U 19 -144.77 -96.46 REMARK 500 ASP U 22 71.58 -156.04 REMARK 500 GLU U 34 -127.95 33.40 REMARK 500 SER U 44 168.00 176.30 REMARK 500 CYS U 45 163.19 -45.69 REMARK 500 THR U 54 -62.43 -126.09 REMARK 500 LEU U 55 122.83 50.97 REMARK 500 ASP U 74 97.07 -45.88 REMARK 500 LEU U 75 104.65 66.42 REMARK 500 CYS U 76 -2.51 -153.65 REMARK 500 GLN U 78 124.03 -27.79 REMARK 500 SER U 81 -179.13 -57.59 REMARK 500 THR U 86 112.80 159.23 REMARK 500 TYR U 92 -120.52 -110.94 REMARK 500 MET U 103 5.99 59.06 REMARK 500 GLN U 131 -102.54 -172.55 REMARK 500 GLU U 135 44.07 178.78 REMARK 500 ARG U 137 166.04 71.91 REMARK 500 PRO U 138 148.39 -33.04 REMARK 500 CYS U 153 -74.12 -118.98 REMARK 500 PRO U 154 125.10 -34.20 REMARK 500 ASN U 162 -34.46 -39.62 REMARK 500 ASP U 163 26.10 -143.26 REMARK 500 CYS U 170 106.03 -167.46 REMARK 500 REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS. 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 GLU U 16 CYS U 17 -137.00 REMARK 500 GLU U 185 ASN U 186 -146.32 REMARK 500 GLU U 230 PRO U 231 -120.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FD6 RELATED DB: PDB REMARK 900 STRUCTURE OF UROKINASE RECEPTOR IN COMPLEX WITH UROKINASE REMARK 900 RELATED ID: 3BT2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH FAB FRAGMENTS DBREF 3BT1 A 1 133 UNP P00749 UROK_HUMAN 21 153 DBREF 3BT1 B 2 41 UNP P04004 VTNC_HUMAN 21 60 DBREF 3BT1 U 1 281 UNP Q03405 UPAR_HUMAN 23 303 SEQADV 3BT1 ARG A -1 UNP P00749 EXPRESSION TAG SEQADV 3BT1 SER A 0 UNP P00749 EXPRESSION TAG SEQADV 3BT1 ARG U -1 UNP Q03405 EXPRESSION TAG SEQADV 3BT1 SER U 0 UNP Q03405 EXPRESSION TAG SEQRES 1 A 135 ARG SER SER ASN GLU LEU HIS GLN VAL PRO SER ASN CYS SEQRES 2 A 135 ASP CYS LEU ASN GLY GLY THR CYS VAL SER ASN LYS TYR SEQRES 3 A 135 PHE SER ASN ILE HIS TRP CYS ASN CYS PRO LYS LYS PHE SEQRES 4 A 135 GLY GLY GLN HIS CYS GLU ILE ASP LYS SER LYS THR CYS SEQRES 5 A 135 TYR GLU GLY ASN GLY HIS PHE TYR ARG GLY LYS ALA SER SEQRES 6 A 135 THR ASP THR MET GLY ARG PRO CYS LEU PRO TRP ASN SER SEQRES 7 A 135 ALA THR VAL LEU GLN GLN THR TYR HIS ALA HIS ARG SER SEQRES 8 A 135 ASP ALA LEU GLN LEU GLY LEU GLY LYS HIS ASN TYR CYS SEQRES 9 A 135 ARG ASN PRO ASP ASN ARG ARG ARG PRO TRP CYS TYR VAL SEQRES 10 A 135 GLN VAL GLY LEU LYS PRO LEU VAL GLN GLU CYS MET VAL SEQRES 11 A 135 HIS ASP CYS ALA ASP SEQRES 1 B 40 GLN GLU SER CYS LYS GLY ARG CYS THR GLU GLY PHE ASN SEQRES 2 B 40 VAL ASP LYS LYS CYS GLN CYS ASP GLU LEU CYS SER TYR SEQRES 3 B 40 TYR GLN SER CYS CYS THR ASP TYR THR ALA GLU CYS LYS SEQRES 4 B 40 PRO SEQRES 1 U 283 ARG SER LEU ARG CYS MET GLN CYS LYS THR ASN GLY ASP SEQRES 2 U 283 CYS ARG VAL GLU GLU CYS ALA LEU GLY GLN ASP LEU CYS SEQRES 3 U 283 ARG THR THR ILE VAL ARG LEU TRP GLU GLU GLY GLU GLU SEQRES 4 U 283 LEU GLU LEU VAL GLU LYS SER CYS THR HIS SER GLU LYS SEQRES 5 U 283 THR ASN ARG THR LEU SER TYR ARG THR GLY LEU LYS ILE SEQRES 6 U 283 THR SER LEU THR GLU VAL VAL CYS GLY LEU ASP LEU CYS SEQRES 7 U 283 ASN GLN GLY ASN SER GLY ARG ALA VAL THR TYR SER ARG SEQRES 8 U 283 SER ARG TYR LEU GLU CYS ILE SER CYS GLY SER SER ASP SEQRES 9 U 283 MET SER CYS GLU ARG GLY ARG HIS GLN SER LEU GLN CYS SEQRES 10 U 283 ARG SER PRO GLU GLU GLN CYS LEU ASP VAL VAL THR HIS SEQRES 11 U 283 TRP ILE GLN GLU GLY GLU GLU GLY ARG PRO LYS ASP ASP SEQRES 12 U 283 ARG HIS LEU ARG GLY CYS GLY TYR LEU PRO GLY CYS PRO SEQRES 13 U 283 GLY SER ASN GLY PHE HIS ASN ASN ASP THR PHE HIS PHE SEQRES 14 U 283 LEU LYS CYS CYS ASN THR THR LYS CYS ASN GLU GLY PRO SEQRES 15 U 283 ILE LEU GLU LEU GLU ASN LEU PRO GLN ASN GLY ARG GLN SEQRES 16 U 283 CYS TYR SER CYS LYS GLY ASN SER THR HIS GLY CYS SER SEQRES 17 U 283 SER GLU GLU THR PHE LEU ILE ASP CYS ARG GLY PRO MET SEQRES 18 U 283 ASN GLN CYS LEU VAL ALA THR GLY THR HIS GLU PRO LYS SEQRES 19 U 283 ASN GLN SER TYR MET VAL ARG GLY CYS ALA THR ALA SER SEQRES 20 U 283 MET CYS GLN HIS ALA HIS LEU GLY ASP ALA PHE SER MET SEQRES 21 U 283 ASN HIS ILE ASP VAL SER CYS CYS THR LYS SER GLY CYS SEQRES 22 U 283 ASN HIS PRO ASP LEU ASP VAL GLN TYR ARG MODRES 3BT1 ASN U 52 ASN GLYCOSYLATION SITE MODRES 3BT1 ASN U 172 ASN GLYCOSYLATION SITE MODRES 3BT1 ASN U 200 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET MAN C 3 11 HET NAG U1052 14 HET NAG U1172 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 NAG 4(C8 H15 N O6) FORMUL 4 MAN C6 H12 O6 HELIX 1 1 THR A 78 GLN A 82 5 5 HELIX 2 2 ARG A 88 GLN A 93 5 6 HELIX 3 3 LEU B 24 GLN B 29 1 6 HELIX 4 4 ASP B 34 CYS B 39 1 6 HELIX 5 5 SER U 101 MET U 103 5 3 HELIX 6 6 SER U 206 THR U 210 5 5 HELIX 7 7 HIS U 251 PHE U 256 1 6 SHEET 1 A 2 THR A 18 SER A 21 0 SHEET 2 A 2 HIS A 29 ASN A 32 -1 O TRP A 30 N VAL A 20 SHEET 1 B 2 PHE A 37 GLY A 38 0 SHEET 2 B 2 ILE A 44 ASP A 45 -1 O ILE A 44 N GLY A 38 SHEET 1 C 2 CYS A 50 TYR A 51 0 SHEET 2 C 2 HIS A 129 ASP A 130 1 O HIS A 129 N TYR A 51 SHEET 1 D 2 TRP A 112 VAL A 115 0 SHEET 2 D 2 LEU A 122 GLU A 125 -1 O GLN A 124 N CYS A 113 SHEET 1 E 2 ARG U 2 CYS U 6 0 SHEET 2 E 2 CYS U 12 GLU U 16 -1 O GLU U 15 N CYS U 3 SHEET 1 F 4 GLU U 36 THR U 46 0 SHEET 2 F 4 LEU U 23 GLU U 33 -1 N GLU U 33 O GLU U 36 SHEET 3 F 4 LYS U 62 CYS U 71 -1 O THR U 67 N ILE U 28 SHEET 4 F 4 SER U 56 THR U 59 -1 N TYR U 57 O THR U 64 SHEET 1 G 9 GLN U 111 GLN U 114 0 SHEET 2 G 9 GLU U 94 GLY U 99 -1 N CYS U 95 O LEU U 113 SHEET 3 G 9 HIS U 143 GLY U 148 -1 O ARG U 145 N CYS U 98 SHEET 4 G 9 GLN U 121 TRP U 129 -1 N GLN U 121 O GLY U 148 SHEET 5 G 9 THR U 164 CYS U 171 -1 O PHE U 165 N HIS U 128 SHEET 6 G 9 GLY U 155 ASN U 161 -1 N ASN U 157 O LEU U 168 SHEET 7 G 9 MET U 237 ALA U 242 -1 O CYS U 241 N HIS U 160 SHEET 8 G 9 GLN U 221 HIS U 229 -1 N GLN U 221 O ALA U 242 SHEET 9 G 9 MET U 258 CYS U 266 -1 O CYS U 266 N CYS U 222 SHEET 1 H 2 GLN U 189 SER U 196 0 SHEET 2 H 2 PHE U 211 ARG U 216 -1 O ILE U 213 N CYS U 194 SSBOND 1 CYS A 11 CYS A 19 1555 1555 2.01 SSBOND 2 CYS A 13 CYS A 31 1555 1555 2.03 SSBOND 3 CYS A 33 CYS A 42 1555 1555 2.02 SSBOND 4 CYS A 50 CYS A 131 1555 1555 2.04 SSBOND 5 CYS A 71 CYS A 113 1555 1555 2.03 SSBOND 6 CYS A 102 CYS A 126 1555 1555 2.04 SSBOND 7 CYS B 5 CYS B 21 1555 1555 2.03 SSBOND 8 CYS B 9 CYS B 39 1555 1555 2.01 SSBOND 9 CYS B 19 CYS B 32 1555 1555 2.08 SSBOND 10 CYS B 25 CYS B 31 1555 1555 2.01 SSBOND 11 CYS U 3 CYS U 24 1555 1555 2.06 SSBOND 12 CYS U 6 CYS U 12 1555 1555 2.02 SSBOND 13 CYS U 17 CYS U 45 1555 1555 2.04 SSBOND 14 CYS U 71 CYS U 76 1555 1555 2.05 SSBOND 15 CYS U 95 CYS U 122 1555 1555 1.98 SSBOND 16 CYS U 98 CYS U 105 1555 1555 2.04 SSBOND 17 CYS U 115 CYS U 147 1555 1555 2.08 SSBOND 18 CYS U 153 CYS U 170 1555 1555 2.00 SSBOND 19 CYS U 171 CYS U 176 1555 1555 2.04 SSBOND 20 CYS U 194 CYS U 222 1555 1555 1.97 SSBOND 21 CYS U 197 CYS U 205 1555 1555 2.08 SSBOND 22 CYS U 215 CYS U 241 1555 1555 2.01 SSBOND 23 CYS U 247 CYS U 265 1555 1555 2.03 SSBOND 24 CYS U 266 CYS U 271 1555 1555 2.04 LINK ND2 ASN U 52 C1 NAG U1052 1555 1555 1.55 LINK ND2 ASN U 172 C1 NAG U1172 1555 1555 1.33 LINK ND2 ASN U 200 C1 NAG C 1 1555 1555 1.47 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.47 LINK O4 NAG C 2 C1 MAN C 3 1555 1555 1.48 CRYST1 97.353 105.187 55.360 90.00 90.00 90.00 P 21 21 2 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 0.010272 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018064 0.00000