PDB Short entry for 3KHV HEADER HYDROLASE 30-OCT-09 3KHV TITLE CRYSTAL STRUCTURES OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR IN COMPLEX TITLE 2 WITH 4-(AMINOMETHYL) BENZOIC ACID AND 4-(AMINOMETHYL-PHENYL)-METHANOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 179-431; COMPND 5 SYNONYM: U-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN COMPND 6 ACTIVATOR CHAIN B; COMPND 7 EC: 3.4.21.73; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: 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: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X-33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA KEYWDS PROTEIN-LIGAND COMPLEX, DISULFIDE BOND, FIBRINOLYSIS, HYDROLASE, KEYWDS 2 PLASMINOGEN ACTIVATION, SERINE PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR L.-G.JIANG,G.-X.ZHAO,X.-B.BIAN,C.YUAN,Z.-X.HUANG,M.-D.HUANG REVDAT 3 10-NOV-21 3KHV 1 REMARK SEQADV REVDAT 2 25-DEC-19 3KHV 1 REMARK REVDAT 1 01-DEC-09 3KHV 0 JRNL AUTH L.-G.JIANG,G.-X.ZHAO,X.-B.BIAN,C.YUAN,Z.-X.HUANG,M.-D.HUANG JRNL TITL CRYSTAL STRUCTURES OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR JRNL TITL 2 IN COMPLEX WITH 4-(AMINOMETHYL) BENZOIC ACID AND JRNL TITL 3 4-(AMINOMETHYL-PHENYL)-METHANOL JRNL REF CHIN.J.STRUCT.CHEM. V. 28 253 2009 JRNL REFN ISSN 0254-5861 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1769943.900 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 9238 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 SET) : 0.228 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 968 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1203 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.57000 REMARK 3 B22 (A**2) : -3.57000 REMARK 3 B33 (A**2) : 7.14000 REMARK 3 B12 (A**2) : 0.74000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.48 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 96.88 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : AMP_PAR.TXT REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9307 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 39.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.240 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09510 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.56 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2NWN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M SODIUM CITRATE, 1.95M (NH4)2SO4, REMARK 280 0.05% NAN3, 5% PEG 400, PH 4.60, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 60.41300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.87946 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.11833 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.41300 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 34.87946 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.11833 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.41300 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 34.87946 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.11833 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.75892 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.23667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.75892 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.23667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.75892 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 28.23667 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HIS A 37 REMARK 465 ARG A 37A REMARK 465 GLY A 37B REMARK 465 GLY A 37C REMARK 465 ASP A 97 REMARK 465 THR A 97A REMARK 465 LEU A 97B REMARK 465 GLU A 244 REMARK 465 GLU A 245 REMARK 465 ASN A 246 REMARK 465 GLY A 247 REMARK 465 LEU A 248 REMARK 465 ALA A 249 REMARK 465 LEU A 250 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 320 O HOH A 360 0.65 REMARK 500 O VAL A 38 CG2 THR A 39 1.76 REMARK 500 O HOH A 274 O HOH A 314 1.92 REMARK 500 O ASP A 185 O HOH A 299 1.93 REMARK 500 O HOH A 263 O HOH A 424 1.98 REMARK 500 O HOH A 274 O HOH A 424 2.01 REMARK 500 N PHE A 21 O HOH A 259 2.04 REMARK 500 O HOH A 390 O HOH A 422 2.09 REMARK 500 O HOH A 259 O HOH A 439 2.10 REMARK 500 O HOH A 283 O HOH A 302 2.11 REMARK 500 OE1 GLN A 145 O HOH A 469 2.12 REMARK 500 O HOH A 343 O HOH A 356 2.13 REMARK 500 O HOH A 386 O HOH A 461 2.17 REMARK 500 O HOH A 274 O HOH A 412 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 300 O HOH A 313 1556 1.24 REMARK 500 O HOH A 257 O HOH A 399 6465 1.37 REMARK 500 O HOH A 9 O HOH A 399 6465 1.44 REMARK 500 O HOH A 382 O HOH A 382 2665 1.59 REMARK 500 O HOH A 259 O HOH A 469 6465 1.84 REMARK 500 OE2 GLU A 110B O HOH A 415 8665 1.91 REMARK 500 NE2 GLN A 78 O HOH A 438 8665 2.04 REMARK 500 O HOH A 15 O HOH A 390 6464 2.09 REMARK 500 O HOH A 458 O HOH A 482 8665 2.10 REMARK 500 O GLN A 113 O HOH A 482 8665 2.10 REMARK 500 O HOH A 355 O HOH A 375 8664 2.13 REMARK 500 O HOH A 3 O HOH A 310 1556 2.19 REMARK 500 O HOH A 439 O HOH A 465 8664 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 ARG A 35 C ARG A 35 O -0.137 REMARK 500 ARG A 36 CZ ARG A 36 NH1 -0.096 REMARK 500 ARG A 36 CZ ARG A 36 NH2 -0.140 REMARK 500 ARG A 36 C ARG A 36 O -0.132 REMARK 500 THR A 39 N THR A 39 CA 0.134 REMARK 500 THR A 39 CB THR A 39 CG2 -0.225 REMARK 500 TYR A 40 CD1 TYR A 40 CE1 -0.192 REMARK 500 TYR A 40 CZ TYR A 40 CE2 -0.149 REMARK 500 TYR A 40 CE2 TYR A 40 CD2 -0.104 REMARK 500 TYR A 40 C TYR A 40 O -0.130 REMARK 500 SER A 110 CB SER A 110 OG -0.096 REMARK 500 SER A 110 CA SER A 110 C -0.177 REMARK 500 GLU A 110B CD GLU A 110B OE2 -0.098 REMARK 500 ARG A 110D CG ARG A 110D CD 0.166 REMARK 500 CYS A 111 C CYS A 111 O -0.205 REMARK 500 GLN A 170 CB GLN A 170 CG -0.185 REMARK 500 GLN A 170 CG GLN A 170 CD -0.179 REMARK 500 GLN A 170 CA GLN A 170 C -0.192 REMARK 500 GLN A 170 C GLN A 170 O -0.159 REMARK 500 PRO A 170A C PRO A 170A O -0.139 REMARK 500 TYR A 171 CD1 TYR A 171 CE1 -0.095 REMARK 500 TYR A 171 CZ TYR A 171 CE2 -0.093 REMARK 500 TYR A 171 CE2 TYR A 171 CD2 -0.120 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 36 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 36 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 VAL A 38 C - N - CA ANGL. DEV. = -18.7 DEGREES REMARK 500 THR A 39 N - CA - C ANGL. DEV. = 21.5 DEGREES REMARK 500 ARG A 110D NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 111 CB - CA - C ANGL. DEV. = 8.8 DEGREES REMARK 500 CYS A 111 CA - CB - SG ANGL. DEV. = 18.8 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 55.52 -153.77 REMARK 500 VAL A 38 113.19 90.97 REMARK 500 THR A 39 142.43 140.14 REMARK 500 VAL A 41 -63.65 -102.15 REMARK 500 SER A 54 -154.02 -151.63 REMARK 500 SER A 115 -165.32 -166.32 REMARK 500 MET A 126 128.50 -36.21 REMARK 500 TYR A 171 -115.07 -61.81 REMARK 500 TRP A 186 19.64 58.70 REMARK 500 ASP A 189 177.47 177.11 REMARK 500 SER A 214 -56.38 -122.91 REMARK 500 ASP A 223A 19.80 56.10 REMARK 500 ARG A 230 94.13 -66.78 REMARK 500 SER A 232 4.18 -69.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 37D -22.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE WATER MOLECULE S205 DESCRIBED IN THE ASSOCIATED ARTICLE IS REMARK 600 CALLED AS A 449 IN THIS ENTRY. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4AL A 4069 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 5115 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NWN RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH UPAIN-1 REMARK 900 RELATED ID: 3KGP RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH 4-(AMINOMETHYL) BENZOIC ACID REMARK 900 RELATED ID: 3KID RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH ETHYL 2-AMINO-1,3-BENZOTHIAZOLE-6- REMARK 900 CARBOXYLATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PDB IS NUMBERED BY CHYMOTRYPSINOGEN NUMBERING OF SERINE REMARK 999 PROTEINASES AND THUS INCLUDES INSERTION CODES. DBREF 3KHV A 16 250 UNP P00749 UROK_HUMAN 179 431 SEQADV 3KHV ALA A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQADV 3KHV GLN A 145 UNP P00749 ASN 322 ENGINEERED MUTATION SEQRES 1 A 253 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 A 253 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 A 253 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 A 253 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 A 253 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 A 253 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 A 253 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 A 253 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 A 253 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 A 253 GLN THR ILE ALA LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 A 253 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 A 253 GLN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 A 253 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 A 253 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 A 253 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 A 253 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 A 253 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 A 253 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 A 253 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS GLU SEQRES 20 A 253 GLU ASN GLY LEU ALA LEU HET 4AL A4069 10 HET SO4 A 402 5 HET PGE A5115 10 HETNAM 4AL [4-(AMINOMETHYL)PHENYL]METHANOL HETNAM SO4 SULFATE ION HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 4AL C8 H11 N O FORMUL 3 SO4 O4 S 2- FORMUL 4 PGE C6 H14 O4 FORMUL 5 HOH *260(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 170 1 7 HELIX 5 5 PHE A 234 HIS A 241 1 8 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 ALA A 184 N LYS A 161 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 GLY A 216 -1 N TRP A 215 O VAL A 227 SHEET 6 A 8 PRO A 198 SER A 202 -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 LYS A 156 N GLY A 140 SHEET 1 B 7 PHE A 30 ARG A 35 0 SHEET 2 B 7 TYR A 40 SER A 48 -1 O GLY A 44 N ALA A 31 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 ALA A 104 N SER A 54 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 35 -1 N TYR A 34 O ILE A 65 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 50 CYS A 111 1555 1555 1.24 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.02 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.04 SITE 1 AC1 7 ASP A 189 SER A 190 CYS A 191 GLN A 192 SITE 2 AC1 7 GLY A 219 GLY A 226 SO4 A 402 SITE 1 AC2 6 HIS A 57 GLN A 192 GLY A 193 SER A 195 SITE 2 AC2 6 HOH A 442 4AL A4069 SITE 1 AC3 7 GLY A 133 LEU A 162 ILE A 163 ALA A 184 SITE 2 AC3 7 ASP A 185 PRO A 185A TRP A 186 CRYST1 120.826 120.826 42.355 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 0.008276 0.004778 0.000000 0.00000 SCALE2 0.000000 0.009557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023610 0.00000