HEADER HYDROLASE 05-MAY-04 1VYQ TITLE NOVEL INHIBITORS OF PLASMODIUM FALCIPARUM DUTPASE PROVIDE A PLATFORM TITLE 2 FOR ANTI-MALARIAL DRUG DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DUTP PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: INHIBITOR COMPLEX SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11PFDUT KEYWDS DRUG DESIGN, PLASMODIUM FALCIPARUM, DUTPASE, DEOXYURIDINE KEYWDS 2 NUCLEOTIDOHYDROLASE, MALARIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.WHITTINGHAM,I.LEAL,G.KASINATHAN,C.NGUYEN,E.BELL,A.F.JONES, AUTHOR 2 C.BERRY,A.BENITO,J.P.TURKENBURG,E.J.DODSON,L.M.RUIZ PEREZ, AUTHOR 3 A.J.WILKINSON,N.G.JOHANSSON,R.BRUN,I.H.GILBERT,D.GONZALEZ AUTHOR 4 PACANOWSKA,K.S.WILSON REVDAT 3 13-DEC-23 1VYQ 1 REMARK REVDAT 2 24-FEB-09 1VYQ 1 VERSN REVDAT 1 26-MAY-05 1VYQ 0 JRNL AUTH J.L.WHITTINGHAM,I.LEAL,C.NGUYEN,G.KASINATHAN,E.BELL, JRNL AUTH 2 A.F.JONES,C.BERRY,A.BENITO,J.P.TURKENBURG,E.J.DODSON, JRNL AUTH 3 L.M.RUIZ PEREZ,A.J.WILKINSON,N.G.JOHANSSON,R.BRUN, JRNL AUTH 4 I.H.GILBERT,D.GONZALEZ PACANOWSKA,K.S.WILSON JRNL TITL DUTPASE AS A PLATFORM FOR ANTIMALARIAL DRUG DESIGN: JRNL TITL 2 STRUCTURAL BASIS FOR THE SELECTIVITY OF A CLASS OF JRNL TITL 3 NUCLEOSIDE INHIBITORS. JRNL REF STRUCTURE V. 13 329 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15698576 JRNL DOI 10.1016/J.STR.2004.11.015 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18324 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 934 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.28000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -2.50000 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): 0.431 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.318 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.237 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.347 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: ATOMS WITH ZERO OCCUPANCY WERE REMOVED REMARK 3 DURING PDB DEPOSITION REMARK 4 REMARK 4 1VYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290015163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 7.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18324 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.66900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1MQ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN SOLUTION CONTAINING 3 REMARK 280 -FOLD EXCESS OF INHIBITOR. 0.1 M HEPES PH 7.1, 25% W/W PEG-MME REMARK 280 2000, 0.8 M SODIUM FORMATE, PH 7.10 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 60.76350 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 30.38175 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 91.14525 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A 25 REMARK 465 TYR A 64 REMARK 465 LYS A 65 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 ARG A 160 REMARK 465 GLY A 161 REMARK 465 GLU A 162 REMARK 465 GLY A 163 REMARK 465 GLY A 164 REMARK 465 PHE A 165 REMARK 465 GLY A 166 REMARK 465 SER A 167 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 CYS B 66 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 LEU B 155 REMARK 465 ASP B 156 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 C 24 REMARK 465 GLY C 25 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 ASP C 156 REMARK 465 GLU C 157 REMARK 465 THR C 158 REMARK 465 SER C 159 REMARK 465 ARG C 160 REMARK 465 GLY C 161 REMARK 465 GLU C 162 REMARK 465 GLY C 163 REMARK 465 GLY C 164 REMARK 465 PHE C 165 REMARK 465 GLY C 166 REMARK 465 SER C 167 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 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 GLU A 14 CB CG CD OE1 OE2 REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 LYS A 20 CB CG CD CE NZ REMARK 470 HIS A 23 ND1 CD2 CE1 NE2 REMARK 470 GLU A 24 CA C O CB CG CD OE1 REMARK 470 GLU A 24 OE2 REMARK 470 LYS A 35 CD CE NZ REMARK 470 LYS A 40 CE NZ REMARK 470 LYS A 59 CE NZ REMARK 470 SER A 60 CB OG REMARK 470 ASN A 61 CB CG OD1 ND2 REMARK 470 TYR A 62 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 62 OH REMARK 470 TYR A 63 C O CB CG CD1 CD2 CE1 REMARK 470 TYR A 63 CE2 CZ OH REMARK 470 ASN A 80 N CA CB CG OD1 ND2 REMARK 470 GLN A 126 CD OE1 NE2 REMARK 470 ASP A 156 CB CG OD1 OD2 REMARK 470 THR A 158 CB OG1 CG2 REMARK 470 SER A 159 CA C O CB OG REMARK 470 LYS B 4 CD CE NZ REMARK 470 ASP B 10 CG OD1 OD2 REMARK 470 GLU B 11 CG CD OE1 OE2 REMARK 470 ARG B 13 CZ NH1 NH2 REMARK 470 GLU B 14 CB CG CD OE1 OE2 REMARK 470 LYS B 17 CE NZ REMARK 470 LYS B 20 CB CG CD CE NZ REMARK 470 HIS B 23 CB CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 24 CB CG CD OE1 OE2 REMARK 470 ASP B 26 CB CG OD1 OD2 REMARK 470 LYS B 35 CB CG CD CE NZ REMARK 470 LYS B 40 CB CG CD CE NZ REMARK 470 LYS B 42 CD CE NZ REMARK 470 LYS B 48 CD CE NZ REMARK 470 ILE B 51 CD1 REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 ILE B 54 CG1 CG2 CD1 REMARK 470 GLN B 57 CB CG CD OE1 NE2 REMARK 470 TYR B 58 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR B 58 OH REMARK 470 LYS B 59 CB CG CD CE NZ REMARK 470 LYS B 65 C O CB CG CD CE NZ REMARK 470 ASN B 80 N CB CG OD1 ND2 REMARK 470 VAL B 82 CB CG1 CG2 REMARK 470 ASN B 83 CG OD1 ND2 REMARK 470 LYS B 96 CD CE NZ REMARK 470 ARG B 113 CZ NH1 NH2 REMARK 470 ASP B 125 CG OD1 OD2 REMARK 470 LYS B 131 CE NZ REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 GLU B 153 CG CD OE1 OE2 REMARK 470 GLU B 154 CB CG CD OE1 OE2 REMARK 470 GLU C 11 CB CG CD OE1 OE2 REMARK 470 ARG C 13 CD NE CZ NH1 NH2 REMARK 470 LYS C 17 CG CD CE NZ REMARK 470 ASN C 18 CG OD1 ND2 REMARK 470 LYS C 20 CB CG CD CE NZ REMARK 470 THR C 21 CB OG1 CG2 REMARK 470 HIS C 22 CB CG ND1 CD2 CE1 NE2 REMARK 470 HIS C 23 CA C O CB CG ND1 CD2 REMARK 470 HIS C 23 CE1 NE2 REMARK 470 ASP C 26 CB CG OD1 OD2 REMARK 470 LYS C 35 CG CD CE NZ REMARK 470 LYS C 42 CD CE NZ REMARK 470 LYS C 59 CB CG CD CE NZ REMARK 470 LYS C 65 CE NZ REMARK 470 LYS C 78 CB CG CD CE NZ REMARK 470 LYS C 96 CE NZ REMARK 470 LYS C 131 CD CE NZ REMARK 470 GLU C 145 CG CD OE1 OE2 REMARK 470 GLU C 153 CD OE1 OE2 REMARK 470 GLU C 154 CB CG CD OE1 OE2 REMARK 470 LEU C 155 CA C O CB CG CD1 CD2 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 OG SER B 27 O GLY B 144 2.06 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 ASP A 10 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 121 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 HIS B 23 C - N - CA ANGL. DEV. = -31.0 DEGREES REMARK 500 ASP B 26 C - N - CA ANGL. DEV. = -19.0 DEGREES REMARK 500 ASP B 26 CA - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 ASP B 26 O - C - N ANGL. DEV. = 14.1 DEGREES REMARK 500 ASP B 30 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 109 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP B 121 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP C 26 CA - C - N ANGL. DEV. = -20.9 DEGREES REMARK 500 ASP C 26 O - C - N ANGL. DEV. = 14.6 DEGREES REMARK 500 ASP C 30 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP C 36 CB - CG - OD1 ANGL. DEV. = 5.5 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 ASN A 18 42.45 -96.37 REMARK 500 SER A 104 -68.64 62.83 REMARK 500 ASN A 133 -10.60 81.69 REMARK 500 ASN B 18 36.57 -90.60 REMARK 500 LYS B 35 141.86 179.87 REMARK 500 PRO B 41 150.60 -49.44 REMARK 500 ALA B 53 142.03 -176.60 REMARK 500 SER B 104 -66.11 67.37 REMARK 500 ARG B 113 25.76 -145.54 REMARK 500 ASP B 125 31.68 -87.27 REMARK 500 ASN B 133 -2.21 72.68 REMARK 500 ASN C 18 46.48 -99.66 REMARK 500 ALA C 53 119.20 -166.06 REMARK 500 SER C 104 -74.46 67.68 REMARK 500 ASN C 133 -6.34 77.46 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 HIS B 23 GLU B 24 -140.58 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 HIS B 23 14.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2021 DISTANCE = 6.25 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUX A1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUX B1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUX C1160 DBREF 1VYQ A 1 173 UNP Q8II92 Q8II92 1 173 DBREF 1VYQ B 1 173 UNP Q8II92 Q8II92 1 173 DBREF 1VYQ C 1 173 UNP Q8II92 Q8II92 1 173 SEQRES 1 A 173 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 A 173 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 A 173 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 A 173 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 A 173 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 A 173 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 A 173 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 A 173 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 A 173 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 A 173 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 A 173 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 A 173 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 A 173 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 A 173 ASN ASN LYS TYR SEQRES 1 B 173 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 B 173 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 B 173 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 B 173 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 B 173 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 B 173 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 B 173 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 B 173 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 B 173 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 B 173 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 B 173 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 B 173 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 B 173 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 B 173 ASN ASN LYS TYR SEQRES 1 C 173 MET HIS LEU LYS ILE VAL CYS LEU SER ASP GLU VAL ARG SEQRES 2 C 173 GLU MET TYR LYS ASN HIS LYS THR HIS HIS GLU GLY ASP SEQRES 3 C 173 SER GLY LEU ASP LEU PHE ILE VAL LYS ASP GLU VAL LEU SEQRES 4 C 173 LYS PRO LYS SER THR THR PHE VAL LYS LEU GLY ILE LYS SEQRES 5 C 173 ALA ILE ALA LEU GLN TYR LYS SER ASN TYR TYR TYR LYS SEQRES 6 C 173 CYS GLU LYS SER GLU ASN LYS LYS LYS ASP ASP ASP LYS SEQRES 7 C 173 SER ASN ILE VAL ASN THR SER PHE LEU LEU PHE PRO ARG SEQRES 8 C 173 SER SER ILE SER LYS THR PRO LEU ARG LEU ALA ASN SER SEQRES 9 C 173 ILE GLY LEU ILE ASP ALA GLY TYR ARG GLY GLU ILE ILE SEQRES 10 C 173 ALA ALA LEU ASP ASN THR SER ASP GLN GLU TYR HIS ILE SEQRES 11 C 173 LYS LYS ASN ASP LYS LEU VAL GLN LEU VAL SER PHE THR SEQRES 12 C 173 GLY GLU PRO LEU SER PHE GLU LEU VAL GLU GLU LEU ASP SEQRES 13 C 173 GLU THR SER ARG GLY GLU GLY GLY PHE GLY SER THR SER SEQRES 14 C 173 ASN ASN LYS TYR HET DUX A1160 35 HET DUX B1160 35 HET DUX C1160 35 HETNAM DUX 2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE HETSYN DUX 1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY) HETSYN 2 DUX METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)- HETSYN 3 DUX DIONE FORMUL 4 DUX 3(C28 H25 F N2 O4) FORMUL 7 HOH *119(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 AA 4 ILE A 81 ASN A 83 0 SHEET 2 AA 4 SER A 43 TYR A 58 -1 O GLN A 57 N VAL A 82 SHEET 3 AA 4 HIS A 2 CYS A 7 -1 O HIS A 2 N LEU A 56 SHEET 4 AA 4 SER A 148 LEU A 151 1 O SER A 148 N LEU A 3 SHEET 1 AB 4 ILE A 81 ASN A 83 0 SHEET 2 AB 4 SER A 43 TYR A 58 -1 O GLN A 57 N VAL A 82 SHEET 3 AB 4 GLU A 115 ASN A 122 -1 O ILE A 116 N LEU A 49 SHEET 4 AB 4 LEU A 99 LEU A 101 -1 O ARG A 100 N ASP A 121 SHEET 1 AC 4 GLY A 28 LEU A 31 0 SHEET 2 AC 4 VAL A 137 VAL A 140 -1 O VAL A 137 N LEU A 31 SHEET 3 AC 4 PHE A 86 PRO A 90 -1 O LEU A 87 N VAL A 140 SHEET 4 AC 4 GLY A 106 ILE A 108 -1 O GLY A 106 N LEU A 88 SHEET 1 AD 2 GLU A 37 LEU A 39 0 SHEET 2 AD 2 TYR A 128 ILE A 130 -1 O TYR A 128 N LEU A 39 SHEET 1 BA 4 ILE B 81 THR B 84 0 SHEET 2 BA 4 ILE B 51 TYR B 58 -1 O ALA B 55 N THR B 84 SHEET 3 BA 4 HIS B 2 CYS B 7 -1 O HIS B 2 N LEU B 56 SHEET 4 BA 4 SER B 148 LEU B 151 1 O SER B 148 N LEU B 3 SHEET 1 BB 4 GLY B 28 PHE B 32 0 SHEET 2 BB 4 LYS B 135 VAL B 140 -1 N LEU B 136 O LEU B 31 SHEET 3 BB 4 PHE B 86 PRO B 90 -1 O LEU B 87 N VAL B 140 SHEET 4 BB 4 GLY B 106 ILE B 108 -1 O GLY B 106 N LEU B 88 SHEET 1 BC 2 GLU B 37 LEU B 39 0 SHEET 2 BC 2 TYR B 128 ILE B 130 -1 O TYR B 128 N LEU B 39 SHEET 1 BD 3 SER B 43 LYS B 48 0 SHEET 2 BD 3 ILE B 117 ASN B 122 -1 O ALA B 118 N VAL B 47 SHEET 3 BD 3 LEU B 99 LEU B 101 -1 O ARG B 100 N ASP B 121 SHEET 1 CA 4 ILE C 81 THR C 84 0 SHEET 2 CA 4 ILE C 51 TYR C 58 -1 O ALA C 55 N THR C 84 SHEET 3 CA 4 HIS C 2 CYS C 7 -1 O HIS C 2 N LEU C 56 SHEET 4 CA 4 SER C 148 LEU C 151 1 O SER C 148 N LEU C 3 SHEET 1 CB 4 GLY C 28 LEU C 31 0 SHEET 2 CB 4 VAL C 137 VAL C 140 -1 O VAL C 137 N LEU C 31 SHEET 3 CB 4 PHE C 86 PRO C 90 -1 O LEU C 87 N VAL C 140 SHEET 4 CB 4 GLY C 106 ILE C 108 -1 O GLY C 106 N LEU C 88 SHEET 1 CC 2 GLU C 37 LEU C 39 0 SHEET 2 CC 2 TYR C 128 ILE C 130 -1 O TYR C 128 N LEU C 39 SHEET 1 CD 3 SER C 43 LYS C 48 0 SHEET 2 CD 3 ILE C 117 ASN C 122 -1 O ALA C 118 N VAL C 47 SHEET 3 CD 3 LEU C 99 LEU C 101 -1 O ARG C 100 N ASP C 121 SITE 1 AC1 11 PHE A 46 LEU A 88 ASN A 103 GLY A 106 SITE 2 AC1 11 TYR A 112 ILE A 117 HOH A2051 SER B 92 SITE 3 AC1 11 SER B 93 LYS C 48 HOH C2017 SITE 1 AC2 9 ASN B 103 GLY B 106 TYR B 112 ILE B 117 SITE 2 AC2 9 ALA B 119 HOH B2025 SER C 92 SER C 95 SITE 3 AC2 9 LYS C 96 SITE 1 AC3 13 VAL A 6 LYS A 52 SER A 92 SER A 95 SITE 2 AC3 13 GLU A 153 PHE C 46 ASN C 103 GLY C 106 SITE 3 AC3 13 TYR C 112 ILE C 116 ILE C 117 ALA C 119 SITE 4 AC3 13 HOH C2042 CRYST1 62.830 62.830 121.527 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 0.015916 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015916 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008229 0.00000