PDB Short entry for 4DW2 HEADER HYDROLASE/IMMUNE SYSTEM 24-FEB-12 4DW2 TITLE THE CRYSTAL STRUCTURE OF UPA IN COMPLEX WITH THE FAB FRAGMENT OF MAB- TITLE 2 112 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: U; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 179-424; COMPND 5 SYNONYM: UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 6 EC: 3.4.21.73; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: FAB FRAGMENT OF PRO-UPA ANTIBODY MAB-112; COMPND 11 CHAIN: H; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: FAB FRAGMENT OF PRO-UPA ANTIBODY MAB-112; COMPND 14 CHAIN: L 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: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZAA; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_TAXID: 10090 KEYWDS UROKINASE-TYPE PLASMINOGEN ACTIVATOR, ANTIBODY, SERINE PROTEASE, KEYWDS 2 ZYMOGEN, HYDROLASE-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.JIANG,K.A.BOTKJAER,L.M.ANDERSEN,C.YUAN,P.A.ANDREASEN,M.HUANG REVDAT 1 16-JAN-13 4DW2 0 JRNL AUTH L.JIANG,K.A.BOTKJAER,L.M.ANDERSEN,C.YUAN,P.A.ANDREASEN, JRNL AUTH 2 M.HUANG JRNL TITL REZYMOGENATION OF ACTIVE UROKINASE INDUCED BY AN INHIBITORY JRNL TITL 2 ANTIBODY. JRNL REF BIOCHEM.J. V. 449 161 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23016918 JRNL DOI 10.1042/BJ20121132 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 10825 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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) : 2.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 651 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : -1.21000 REMARK 3 B33 (A**2) : 0.63000 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): 0.637 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.467 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.884 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.815 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5114 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6920 ; 1.875 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 619 ; 8.646 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;34.615 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 839 ;24.942 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;21.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 778 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3753 ; 0.008 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4DW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB070854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.970 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL 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) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 2000 MME, 100MM TRIS-HCL REMARK 280 (PH 8.0), 0.21M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 19.48050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.38000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.47750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.38000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.48050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.47750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: U, H, L 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 ILE U 16 REMARK 465 ILE U 17 REMARK 465 GLY U 18 REMARK 465 GLY U 19 REMARK 465 GLU U 20 REMARK 465 HIS U 37 REMARK 465 ARG U 37A REMARK 465 GLY U 37B REMARK 465 GLY U 37C REMARK 465 SER U 37D REMARK 465 GLN U 169 REMARK 465 GLN U 170 REMARK 465 PRO U 170A REMARK 465 HIS U 170B REMARK 465 LYS U 187 REMARK 465 THR U 188 REMARK 465 ASP U 189 REMARK 465 SER U 190 REMARK 465 CYS U 191 REMARK 465 GLY U 218 REMARK 465 CYS U 219 REMARK 465 ALA U 220 REMARK 465 LEU U 221 REMARK 465 LYS U 222 REMARK 465 ASP U 223 REMARK 465 GLY H 127 REMARK 465 SER H 128 REMARK 465 HIS L 198 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 VAL U 176 N THR U 178 1.08 REMARK 500 O GLU U 175 N THR U 177 1.34 REMARK 500 CD PRO L 8 CE MET L 11 1.60 REMARK 500 OE1 GLN H 39 NE2 GLN L 38 1.67 REMARK 500 NE ARG H 94 OD2 ASP H 101 1.69 REMARK 500 O TYR U 171 O TYR U 172 1.79 REMARK 500 O PRO H 178 OG1 THR H 181 1.82 REMARK 500 O VAL U 159 OD2 ASP U 185 1.82 REMARK 500 NH2 ARG H 94 OD2 ASP H 101 1.89 REMARK 500 CG PRO L 8 CE MET L 11 1.90 REMARK 500 O TYR L 186 OH TYR L 192 1.95 REMARK 500 CZ ARG H 94 OD2 ASP H 101 1.98 REMARK 500 O VAL L 28 OH TYR L 71 2.02 REMARK 500 OD2 ASP L 151 ND1 HIS L 189 2.03 REMARK 500 O GLN U 131 OG1 THR U 134 2.07 REMARK 500 OG SER H 196 OG1 THR H 198 2.08 REMARK 500 NH1 ARG H 38 OH TYR H 90 2.09 REMARK 500 N SER U 164 OE1 GLU U 167 2.11 REMARK 500 O LEU U 155 NE2 HIS L 31 2.12 REMARK 500 CD1 ILE L 2 O SER L 26 2.12 REMARK 500 OG SER U 164 OE1 GLU U 167 2.13 REMARK 500 N PRO H 178 OG1 THR H 181 2.14 REMARK 500 O LEU U 181 N TYR U 228 2.14 REMARK 500 NH1 ARG U 72 OG SER U 75 2.15 REMARK 500 O VAL U 176 CA THR U 178 2.16 REMARK 500 N LEU H 132 O VAL H 175 2.17 REMARK 500 NE2 GLN H 39 OE1 GLN L 38 2.18 REMARK 500 O ASP L 1 O TYR L 94 2.18 REMARK 500 OE2 GLU H 46 NH2 ARG L 96 2.19 REMARK 500 N GLY H 15 O LEU H 82C 2.19 REMARK 500 O ASP L 184 N GLU L 187 2.19 REMARK 500 O LEU U 150 CA PRO U 152 2.19 REMARK 500 OG SER H 35 OG SER H 50 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 OH TYR U 151 OG SER U 164 1655 1.37 REMARK 500 OG SER L 67 O THR L 200 4445 2.08 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 SER H 82A C SER H 82B N 0.147 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 PRO U 60C C - N - CD ANGL. DEV. = -18.4 DEGREES REMARK 500 PRO U 185A C - N - CD ANGL. DEV. = -18.9 DEGREES REMARK 500 CYS L 23 CA - CB - SG ANGL. DEV. = -10.9 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 PRO U 28 31.29 -93.38 REMARK 500 LEU U 97B -84.53 -109.23 REMARK 500 TYR U 127 59.79 32.71 REMARK 500 THR U 134 155.04 -49.39 REMARK 500 SER U 146 1.48 111.52 REMARK 500 THR U 147 77.63 50.12 REMARK 500 ASP U 148 -176.20 -63.37 REMARK 500 TYR U 172 152.07 46.98 REMARK 500 VAL U 176 4.10 6.25 REMARK 500 THR U 177 -7.73 -17.81 REMARK 500 THR U 178 -16.64 66.13 REMARK 500 LYS H 43 0.51 85.11 REMARK 500 VAL H 63 -1.40 -141.72 REMARK 500 ALA H 88 155.02 179.30 REMARK 500 ALA H 100 166.04 88.12 REMARK 500 SER H 184 -116.76 40.28 REMARK 500 SER H 197 -2.32 66.90 REMARK 500 ILE L 2 77.51 42.09 REMARK 500 ALA L 13 178.24 88.40 REMARK 500 THR L 27A 130.42 32.81 REMARK 500 THR L 51 -64.23 84.12 REMARK 500 ALA L 60 -31.82 -38.47 REMARK 500 ASN L 138 72.11 48.77 REMARK 500 SER L 171 18.28 59.36 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 LEU U 150 TYR U 151 -133.59 REMARK 500 ALA L 13 SER L 14 -126.60 REMARK 500 ALA L 25 SER L 26 147.67 REMARK 500 SER L 26 SER L 27 -148.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 TYR U 149 22.4 L L OUTSIDE RANGE 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 L 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DVB RELATED DB: PDB DBREF 4DW2 U 16 243 UNP P00749 UROK_HUMAN 179 424 DBREF 4DW2 H 1 208 PDB 4DW2 4DW2 1 208 DBREF 4DW2 L 1 214 PDB 4DW2 4DW2 1 214 SEQADV 4DW2 ALA U 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 4DW2 GLN U 145 UNP P00749 ASN 322 ENGINEERED MUTATION SEQRES 1 U 246 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 U 246 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 U 246 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 U 246 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 U 246 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 U 246 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 U 246 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 U 246 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 U 246 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 U 246 GLN THR ILE ALA LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 U 246 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 U 246 GLN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 U 246 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 U 246 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 U 246 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 U 246 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 U 246 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 U 246 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 U 246 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS SEQRES 1 H 212 GLN VAL LYS LEU GLN GLU SER GLY GLY ASP LEU VAL LYS SEQRES 2 H 212 PRO GLY GLY SER LEU LYS LEU SER CYS SER ALA SER GLY SEQRES 3 H 212 PHE THR PHE SER ARG TYR ALA MET SER TRP VAL ARG GLN SEQRES 4 H 212 THR PRO GLU LYS ARG LEU GLU TRP VAL ALA SER ILE THR SEQRES 5 H 212 ASN GLY GLY SER THR TYR TYR SER ASP SER VAL LYS GLY SEQRES 6 H 212 ARG PHE ILE ILE SER ARG ASP ASN ALA ARG ASN ILE LEU SEQRES 7 H 212 SER LEU GLN MET SER SER LEU ARG SER GLU ASP THR ALA SEQRES 8 H 212 MET TYR TYR CYS GLU ARG GLY GLU LEU THR TYR ALA MET SEQRES 9 H 212 ASP TYR TRP GLY GLN GLY THR THR VAL THR VAL SER SER SEQRES 10 H 212 ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO SEQRES 11 H 212 GLY SER MET VAL THR LEU GLY CYS LEU VAL LYS GLY TYR SEQRES 12 H 212 PHE PRO GLU PRO VAL THR VAL THR TRP ASN SER GLY SER SEQRES 13 H 212 LEU SER SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SEQRES 14 H 212 SER ASP LEU TYR THR LEU SER SER SER VAL THR VAL PRO SEQRES 15 H 212 SER SER THR TRP PRO SER GLU THR VAL THR CYS ASN VAL SEQRES 16 H 212 ALA HIS PRO ALA SER SER THR LYS VAL ASP LYS LYS ILE SEQRES 17 H 212 VAL VAL LYS GLY SEQRES 1 L 215 ASP ILE GLU LEU THR GLN SER PRO ALA ILE MET SER ALA SEQRES 2 L 215 SER PRO GLY GLU LYS VAL THR MET THR CYS ARG ALA SER SEQRES 3 L 215 SER THR VAL SER PHE HIS TYR LEU HIS TRP TYR GLN GLN SEQRES 4 L 215 LYS SER GLY ALA SER PRO LYS LEU TRP ILE TYR ALA THR SEQRES 5 L 215 SER ASN LEU ALA SER GLY VAL PRO ALA ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR SER TYR SER LEU THR ILE SER SER SEQRES 7 L 215 VAL GLU THR GLU ASP ALA ALA THR TYR TYR CYS GLN HIS SEQRES 8 L 215 TYR SER ALA TYR PRO ARG THR PHE GLY GLY GLY THR LYS SEQRES 9 L 215 LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER SEQRES 10 L 215 ILE PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY SEQRES 11 L 215 ALA SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS SEQRES 12 L 215 ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG SEQRES 13 L 215 GLN ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER MET SER SER THR LEU THR LEU SEQRES 15 L 215 THR LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS SEQRES 16 L 215 GLU ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SEQRES 17 L 215 SER PHE ASN ARG ASN GLU CYS HET SO4 L 301 5 HETNAM SO4 SULFATE ION FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *10(H2 O) HELIX 1 1 THR U 56 ASP U 60A 1 6 HELIX 2 2 VAL U 231 LYS U 243 1 13 HELIX 3 3 THR H 28 TYR H 32 5 5 HELIX 4 4 ARG H 83 THR H 87 5 5 HELIX 5 5 GLU L 79 ALA L 83 5 5 HELIX 6 6 SER L 121 GLY L 128 1 8 HELIX 7 7 LYS L 183 ARG L 188 1 6 SHEET 1 A 7 THR U 39 CYS U 42 0 SHEET 2 A 7 ALA U 32 ARG U 35 -1 N ARG U 35 O THR U 39 SHEET 3 A 7 TYR U 64 LEU U 68 -1 O ILE U 65 N TYR U 34 SHEET 4 A 7 MET U 81 LEU U 90 -1 O PHE U 83 N VAL U 66 SHEET 5 A 7 ILE U 103 SER U 110 -1 O ARG U 109 N GLU U 84 SHEET 6 A 7 TRP U 51 ALA U 55 -1 N SER U 54 O ALA U 104 SHEET 7 A 7 SER U 45 LEU U 46 -1 N SER U 45 O ILE U 53 SHEET 1 B 2 SER U 95 ALA U 96 0 SHEET 2 B 2 HIS U 99 HIS U 100 -1 O HIS U 100 N SER U 95 SHEET 1 C 7 ARG U 206 LEU U 209 0 SHEET 2 C 7 VAL U 200 LEU U 203 -1 N LEU U 203 O ARG U 206 SHEET 3 C 7 SER U 135 ILE U 138 -1 N GLU U 137 O VAL U 200 SHEET 4 C 7 THR U 158 LEU U 162 -1 O THR U 158 N ILE U 138 SHEET 5 C 7 MET U 180 ALA U 184 -1 O ALA U 184 N LYS U 161 SHEET 6 C 7 GLY U 226 ARG U 230 -1 O TYR U 228 N LEU U 181 SHEET 7 C 7 GLY U 211 TRP U 215 -1 N TRP U 215 O VAL U 227 SHEET 1 D 4 LEU H 4 SER H 7 0 SHEET 2 D 4 LEU H 18 ALA H 24 -1 O SER H 23 N GLN H 5 SHEET 3 D 4 ILE H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 D 4 PHE H 67 ASP H 72 -1 N SER H 70 O SER H 79 SHEET 1 E 5 THR H 57 TYR H 59 0 SHEET 2 E 5 LEU H 45 ILE H 51 -1 N SER H 50 O TYR H 58 SHEET 3 E 5 MET H 34 GLN H 39 -1 N TRP H 36 O ALA H 49 SHEET 4 E 5 ALA H 88 ARG H 94 -1 O TYR H 91 N VAL H 37 SHEET 5 E 5 THR H 107 VAL H 109 -1 O THR H 107 N TYR H 90 SHEET 1 F 4 SER H 120 LEU H 124 0 SHEET 2 F 4 THR H 131 TYR H 139 -1 O LEU H 135 N TYR H 122 SHEET 3 F 4 LEU H 168 THR H 176 -1 O VAL H 175 N LEU H 132 SHEET 4 F 4 VAL H 163 GLN H 165 -1 N GLN H 165 O LEU H 168 SHEET 1 G 3 THR H 145 TRP H 148 0 SHEET 2 G 3 THR H 188 ALA H 192 -1 O ASN H 190 N THR H 147 SHEET 3 G 3 LYS H 199 LYS H 203 -1 O VAL H 200 N VAL H 191 SHEET 1 H 4 LEU L 4 SER L 7 0 SHEET 2 H 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 H 4 SER L 70 ILE L 75 -1 O TYR L 71 N CYS L 23 SHEET 4 H 4 PHE L 62 SER L 67 -1 N SER L 65 O SER L 72 SHEET 1 I 6 ILE L 10 SER L 12 0 SHEET 2 I 6 THR L 102 GLU L 105 1 O GLU L 105 N MET L 11 SHEET 3 I 6 ALA L 84 HIS L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 I 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 I 6 PRO L 44 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 I 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 J 4 THR L 114 PHE L 118 0 SHEET 2 J 4 GLY L 129 PHE L 139 -1 O ASN L 137 N THR L 114 SHEET 3 J 4 TYR L 173 THR L 182 -1 O SER L 177 N CYS L 134 SHEET 4 J 4 VAL L 159 TRP L 163 -1 N SER L 162 O SER L 176 SHEET 1 K 4 SER L 153 ARG L 155 0 SHEET 2 K 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 K 4 SER L 191 THR L 197 -1 O THR L 193 N LYS L 149 SHEET 4 K 4 ILE L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SSBOND 1 CYS U 42 CYS U 58 1555 1555 2.03 SSBOND 2 CYS U 50 CYS U 111 1555 1555 2.00 SSBOND 3 CYS U 136 CYS U 201 1555 1555 1.90 SSBOND 4 CYS U 168 CYS U 182 1555 1555 2.04 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.02 SSBOND 6 CYS H 134 CYS H 189 1555 1555 1.97 SSBOND 7 CYS L 23 CYS L 88 1555 1555 1.99 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.03 CISPEP 1 TYR U 151 PRO U 152 0 -1.05 CISPEP 2 PRO U 185A GLN U 185B 0 18.58 CISPEP 3 PHE H 140 PRO H 141 0 -5.51 CISPEP 4 GLU H 142 PRO H 143 0 2.93 CISPEP 5 TRP H 182 PRO H 183 0 -4.53 CISPEP 6 SER L 7 PRO L 8 0 -5.85 CISPEP 7 TYR L 94 PRO L 95 0 -14.64 CISPEP 8 TYR L 140 PRO L 141 0 -5.21 SITE 1 AC1 5 GLN H 81 THR L 182 ASP L 184 GLU L 185 SITE 2 AC1 5 ARG L 188 CRYST1 38.961 94.955 154.760 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 0.025667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006462 0.00000