HEADER HYDROLASE/HYDROLASE INHIBITOR 29-JUL-11 3T70 TITLE 5'-DIPHENYL NUCLEOSIDE INHIBITORS OF PLASMODIUM FALCIPARUM DUTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, PUTATIVE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 3.6.1.23; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE GLY-HIS-GLY; COMPND 8 CHAIN: F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: PF11_0282; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DUTP BINDING, NUCLEUS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.E.HAMPTON,B.BARAGANA,A.SCHIPANI,C.BOSCH-NAVARRETE,A.MUSSO-BUENDIA, AUTHOR 2 E.RECIO,M.KAISER,J.L.WHITTINGHAM,S.M.ROBERTS,M.SHEVTSOV, AUTHOR 3 J.A.BRANNIGAN,P.KAHNBERG,R.BRUN,K.S.WILSON,D.GONZALEZ-PACANOWSKA, AUTHOR 4 N.G.JOHANSSON,I.H.GILBERT REVDAT 3 01-NOV-23 3T70 1 REMARK SEQADV REVDAT 2 09-OCT-19 3T70 1 SOURCE JRNL REMARK REVDAT 1 29-AUG-12 3T70 0 JRNL AUTH S.E.HAMPTON,B.BARAGANA,A.SCHIPANI,C.BOSCH-NAVARRETE, JRNL AUTH 2 J.A.MUSSO-BUENDIA,E.RECIO,M.KAISER,J.L.WHITTINGHAM, JRNL AUTH 3 S.M.ROBERTS,M.SHEVTSOV,J.A.BRANNIGAN,P.KAHNBERG,R.BRUN, JRNL AUTH 4 K.S.WILSON,D.GONZALEZ-PACANOWSKA,N.G.JOHANSSON,I.H.GILBERT JRNL TITL DESIGN, SYNTHESIS, AND EVALUATION OF 5'-DIPHENYL NUCLEOSIDE JRNL TITL 2 ANALOGUES AS INHIBITORS OF THE PLASMODIUM FALCIPARUM JRNL TITL 3 DUTPASE. JRNL REF CHEMMEDCHEM V. 6 1816 2011 JRNL REFN ESSN 1860-7187 JRNL PMID 22049550 JRNL DOI 10.1002/CMDC.201100255 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0008 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 53806 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2862 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3969 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3458 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.11000 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): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.678 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3772 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5112 ; 1.133 ; 2.023 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 467 ; 6.377 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;33.522 ;24.906 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 701 ;12.531 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.436 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 583 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2744 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1710 ; 0.179 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2507 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 383 ; 0.137 ; 0.200 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): 74 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.157 ; 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): 2316 ; 0.652 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3630 ; 1.115 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1640 ; 1.397 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1461 ; 2.254 ; 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 : 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 3T70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 43.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1VYQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULPHATE, 0.2M DI-SODIUM REMARK 280 PHOSPHATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 52.91500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.45750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.37250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, F 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 THR A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 GLU A 24 REMARK 465 CYS A 66 REMARK 465 GLU A 67 REMARK 465 LYS A 68 REMARK 465 SER A 69 REMARK 465 GLU A 70 REMARK 465 ASN A 71 REMARK 465 LYS A 72 REMARK 465 LYS A 73 REMARK 465 LYS A 74 REMARK 465 ASP A 75 REMARK 465 ASP A 76 REMARK 465 ASP A 77 REMARK 465 LYS A 78 REMARK 465 SER A 79 REMARK 465 THR A 168 REMARK 465 SER A 169 REMARK 465 ASN A 170 REMARK 465 ASN A 171 REMARK 465 LYS A 172 REMARK 465 TYR A 173 REMARK 465 GLU A 174 REMARK 465 ALA A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 LYS B 20 REMARK 465 THR B 21 REMARK 465 HIS B 22 REMARK 465 HIS B 23 REMARK 465 GLU B 24 REMARK 465 GLY B 25 REMARK 465 GLU B 67 REMARK 465 LYS B 68 REMARK 465 SER B 69 REMARK 465 GLU B 70 REMARK 465 ASN B 71 REMARK 465 LYS B 72 REMARK 465 LYS B 73 REMARK 465 LYS B 74 REMARK 465 ASP B 75 REMARK 465 ASP B 76 REMARK 465 ASP B 77 REMARK 465 LYS B 78 REMARK 465 SER B 79 REMARK 465 GLU B 157 REMARK 465 THR B 158 REMARK 465 SER B 159 REMARK 465 ARG B 160 REMARK 465 GLY B 161 REMARK 465 GLU B 162 REMARK 465 GLY B 163 REMARK 465 GLY B 164 REMARK 465 PHE B 165 REMARK 465 GLY B 166 REMARK 465 SER B 167 REMARK 465 THR B 168 REMARK 465 SER B 169 REMARK 465 ASN B 170 REMARK 465 ASN B 171 REMARK 465 LYS B 172 REMARK 465 TYR B 173 REMARK 465 GLU B 174 REMARK 465 ALA B 175 REMARK 465 HIS B 176 REMARK 465 HIS B 177 REMARK 465 HIS B 178 REMARK 465 HIS B 179 REMARK 465 HIS B 180 REMARK 465 HIS B 181 REMARK 465 LYS C 20 REMARK 465 THR C 21 REMARK 465 HIS C 22 REMARK 465 HIS C 23 REMARK 465 GLU C 24 REMARK 465 CYS C 66 REMARK 465 GLU C 67 REMARK 465 LYS C 68 REMARK 465 SER C 69 REMARK 465 GLU C 70 REMARK 465 ASN C 71 REMARK 465 LYS C 72 REMARK 465 LYS C 73 REMARK 465 LYS C 74 REMARK 465 ASP C 75 REMARK 465 ASP C 76 REMARK 465 ASP C 77 REMARK 465 LYS C 78 REMARK 465 SER C 79 REMARK 465 THR C 168 REMARK 465 SER C 169 REMARK 465 ASN C 170 REMARK 465 ASN C 171 REMARK 465 LYS C 172 REMARK 465 TYR C 173 REMARK 465 GLU C 174 REMARK 465 ALA C 175 REMARK 465 HIS C 176 REMARK 465 HIS C 177 REMARK 465 HIS C 178 REMARK 465 HIS C 179 REMARK 465 HIS C 180 REMARK 465 HIS C 181 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP B 156 CG OD1 OD2 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 B 186 O HOH B 188 1.79 REMARK 500 O HOH C 253 O HOH C 254 2.17 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 ASN A 18 58.81 -115.47 REMARK 500 TYR A 64 114.51 -161.13 REMARK 500 SER A 104 -70.76 72.10 REMARK 500 SER A 104 -69.62 71.09 REMARK 500 ASN A 133 -13.42 89.57 REMARK 500 SER B 104 -69.44 70.40 REMARK 500 ASN B 133 -6.48 81.93 REMARK 500 ASN C 18 51.65 -105.79 REMARK 500 ASN C 18 50.72 -105.19 REMARK 500 SER C 104 -70.10 73.20 REMARK 500 ASN C 133 -11.10 84.23 REMARK 500 ASP C 156 -170.93 -170.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH C 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DU4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DU4 B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 183 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 184 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DU4 C 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 183 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T6Y RELATED DB: PDB DBREF 3T70 A 1 173 UNP Q8II92 Q8II92_PLAF7 1 173 DBREF 3T70 B 1 173 UNP Q8II92 Q8II92_PLAF7 1 173 DBREF 3T70 C 1 173 UNP Q8II92 Q8II92_PLAF7 1 173 DBREF 3T70 F 1 3 PDB 3T70 3T70 1 3 SEQADV 3T70 GLU A 174 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 ALA A 175 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 176 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 177 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 178 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 179 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 180 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS A 181 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 GLU B 174 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 ALA B 175 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 176 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 177 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 178 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 179 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 180 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS B 181 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 GLU C 174 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 ALA C 175 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 176 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 177 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 178 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 179 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 180 UNP Q8II92 EXPRESSION TAG SEQADV 3T70 HIS C 181 UNP Q8II92 EXPRESSION TAG SEQRES 1 A 181 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 A 181 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 A 181 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 A 181 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 A 181 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 A 181 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 A 181 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 A 181 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 A 181 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 A 181 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 A 181 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 A 181 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 A 181 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 A 181 ASN ASN LYS TYR GLU ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 181 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 B 181 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 B 181 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 B 181 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 B 181 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 B 181 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 B 181 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 B 181 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 B 181 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 B 181 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 B 181 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 B 181 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 B 181 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 B 181 ASN ASN LYS TYR GLU ALA HIS HIS HIS HIS HIS HIS SEQRES 1 C 181 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 C 181 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 C 181 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 C 181 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 C 181 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 C 181 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 C 181 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 C 181 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 C 181 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 C 181 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 C 181 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 C 181 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 C 181 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 C 181 ASN ASN LYS TYR GLU ALA HIS HIS HIS HIS HIS HIS SEQRES 1 F 3 GLY HIS GLY HET DU4 A 400 30 HET SO4 A 182 5 HET DU4 B 400 30 HET SO4 B 182 5 HET SO4 B 183 5 HET SO4 B 184 5 HET DU4 C 400 30 HET SO4 C 182 5 HET SO4 C 183 5 HETNAM DU4 2',5'-DIDEOXY-5'-[(DIPHENYLMETHYL)(METHYL)AMINO]URIDINE HETNAM SO4 SULFATE ION FORMUL 5 DU4 3(C23 H25 N3 O4) FORMUL 6 SO4 6(O4 S 2-) FORMUL 14 HOH *395(H2 O) HELIX 1 1 SER A 9 ASN A 18 1 10 HELIX 2 2 SER A 92 THR A 97 5 6 HELIX 3 3 SER B 9 ASN B 18 1 10 HELIX 4 4 SER B 92 THR B 97 5 6 HELIX 5 5 SER C 9 ASN C 18 1 10 HELIX 6 6 SER C 92 THR C 97 5 6 SHEET 1 A 4 ILE A 81 THR A 84 0 SHEET 2 A 4 ILE A 51 TYR A 58 -1 N GLN A 57 O VAL A 82 SHEET 3 A 4 HIS A 2 CYS A 7 -1 N HIS A 2 O LEU A 56 SHEET 4 A 4 SER A 148 LEU A 151 1 O GLU A 150 N ILE A 5 SHEET 1 B 4 GLY A 28 PHE A 32 0 SHEET 2 B 4 LYS A 135 VAL A 140 -1 O VAL A 137 N LEU A 31 SHEET 3 B 4 PHE A 86 PRO A 90 -1 N PHE A 89 O GLN A 138 SHEET 4 B 4 GLY A 106 ILE A 108 -1 O ILE A 108 N PHE A 86 SHEET 1 C 2 GLU A 37 LEU A 39 0 SHEET 2 C 2 TYR A 128 ILE A 130 -1 O TYR A 128 N LEU A 39 SHEET 1 D 3 SER A 43 LYS A 48 0 SHEET 2 D 3 ILE A 117 ASN A 122 -1 O ASN A 122 N SER A 43 SHEET 3 D 3 LEU A 99 LEU A 101 -1 N ARG A 100 O ASP A 121 SHEET 1 E 4 ILE B 81 THR B 84 0 SHEET 2 E 4 ILE B 51 TYR B 58 -1 N GLN B 57 O VAL B 82 SHEET 3 E 4 HIS B 2 CYS B 7 -1 N VAL B 6 O LYS B 52 SHEET 4 E 4 SER B 148 LEU B 151 1 O SER B 148 N LEU B 3 SHEET 1 F 4 GLY B 28 PHE B 32 0 SHEET 2 F 4 LYS B 135 VAL B 140 -1 O VAL B 137 N LEU B 31 SHEET 3 F 4 PHE B 86 PRO B 90 -1 N PHE B 89 O GLN B 138 SHEET 4 F 4 GLY B 106 ILE B 108 -1 O ILE B 108 N PHE B 86 SHEET 1 G 2 GLU B 37 LEU B 39 0 SHEET 2 G 2 TYR B 128 ILE B 130 -1 O TYR B 128 N LEU B 39 SHEET 1 H 3 SER B 43 LYS B 48 0 SHEET 2 H 3 ILE B 117 ASN B 122 -1 O ASN B 122 N SER B 43 SHEET 3 H 3 LEU B 99 LEU B 101 -1 N ARG B 100 O ASP B 121 SHEET 1 I 4 ILE C 81 THR C 84 0 SHEET 2 I 4 ILE C 51 TYR C 58 -1 N GLN C 57 O VAL C 82 SHEET 3 I 4 HIS C 2 CYS C 7 -1 N VAL C 6 O LYS C 52 SHEET 4 I 4 SER C 148 LEU C 151 1 O GLU C 150 N ILE C 5 SHEET 1 J 4 GLY C 28 LEU C 31 0 SHEET 2 J 4 VAL C 137 VAL C 140 -1 O VAL C 137 N LEU C 31 SHEET 3 J 4 PHE C 86 PRO C 90 -1 N PHE C 89 O GLN C 138 SHEET 4 J 4 GLY C 106 ILE C 108 -1 O ILE C 108 N PHE C 86 SHEET 1 K 2 GLU C 37 LEU C 39 0 SHEET 2 K 2 TYR C 128 ILE C 130 -1 O TYR C 128 N LEU C 39 SHEET 1 L 3 SER C 43 LYS C 48 0 SHEET 2 L 3 ILE C 117 ASN C 122 -1 O ALA C 118 N VAL C 47 SHEET 3 L 3 LEU C 99 LEU C 101 -1 N ARG C 100 O ASP C 121 CISPEP 1 GLY C 166 SER C 167 0 0.46 SITE 1 AC1 14 PHE A 46 LEU A 88 ASN A 103 GLY A 106 SITE 2 AC1 14 ILE A 108 TYR A 112 ILE A 117 ALA A 119 SITE 3 AC1 14 HOH A 237 HOH A 395 SER B 92 SER B 95 SITE 4 AC1 14 LYS B 96 HOH B 253 SITE 1 AC2 9 ARG A 91 SER A 92 GLN A 138 HOH A 227 SITE 2 AC2 9 HOH A 294 DU4 C 400 HOH C 402 HOH C 506 SITE 3 AC2 9 HOH C 544 SITE 1 AC3 14 PHE B 46 LEU B 88 ASN B 103 GLY B 106 SITE 2 AC3 14 LEU B 107 ILE B 108 TYR B 112 ILE B 116 SITE 3 AC3 14 ILE B 117 ALA B 119 HOH B 236 SER C 92 SITE 4 AC3 14 SO4 C 182 HOH C 222 SITE 1 AC4 8 HOH A 382 ARG B 91 SER B 92 GLN B 138 SITE 2 AC4 8 HOH B 193 HOH B 194 HOH B 253 HOH B 377 SITE 1 AC5 6 ASN A 61 HOH A 245 GLN B 126 GLU B 127 SITE 2 AC5 6 HOH B 204 HOH B 428 SITE 1 AC6 2 LYS B 132 ASN B 133 SITE 1 AC7 14 SER A 92 SO4 A 182 LEU C 88 ASN C 103 SITE 2 AC7 14 GLY C 106 LEU C 107 TYR C 112 ILE C 116 SITE 3 AC7 14 ILE C 117 ALA C 119 HOH C 278 HOH C 402 SITE 4 AC7 14 HOH C 530 HOH C 545 SITE 1 AC8 9 HOH B 359 DU4 B 400 ARG C 91 SER C 92 SITE 2 AC8 9 GLN C 138 HOH C 222 HOH C 268 HOH C 512 SITE 3 AC8 9 HOH C 514 SITE 1 AC9 4 GLY C 111 TYR C 112 ARG C 113 ARG C 160 CRYST1 76.750 76.750 105.830 90.00 90.00 90.00 P 41 12 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 0.013029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009449 0.00000