HEADER HYDROLASE 16-MAR-14 4P5D TITLE CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE- TITLE 2 MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1; COMPND 3 CHAIN: C, A; COMPND 4 FRAGMENT: RESIDUES 11-151; COMPND 5 SYNONYM: DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE,C-MYC- COMPND 6 RESPONSIVE PROTEIN RCL; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: DNPH1, RCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BLI5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS N-GLYCOSIDASE, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PADILLA,G.LABESSE,P.A.KAMINSKI REVDAT 2 20-DEC-23 4P5D 1 REMARK REVDAT 1 20-AUG-14 4P5D 0 JRNL AUTH C.AMIABLE,J.PAOLETTI,A.HAOUZ,A.PADILLA,G.LABESSE, JRNL AUTH 2 P.A.KAMINSKI,S.POCHET JRNL TITL 6-(HETERO)ARYLPURINE NUCLEOTIDES AS INHIBITORS OF THE JRNL TITL 2 ONCOGENIC TARGET DNPH1: SYNTHESIS, STRUCTURAL STUDIES AND JRNL TITL 3 CYTOTOXIC ACTIVITIES. JRNL REF EUR.J.MED.CHEM. V. 85C 418 2014 JRNL REFN ISSN 0223-5234 JRNL PMID 25108359 JRNL DOI 10.1016/J.EJMECH.2014.07.110 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.PADILLA,C.AMIABLE,S.POCHET,P.A.KAMINSKI,G.LABESSE REMARK 1 TITL STRUCTURE OF THE ONCOPROTEIN RCL BOUND TO THREE NUCLEOTIDE REMARK 1 TITL 2 ANALOGUES. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 69 247 2013 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 23385460 REMARK 1 DOI 10.1107/S0907444912045039 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1560 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.1717 - 4.6887 0.99 2864 150 0.1797 0.1981 REMARK 3 2 4.6887 - 3.7226 0.99 2735 140 0.1394 0.1443 REMARK 3 3 3.7226 - 3.2523 0.99 2668 158 0.1703 0.1946 REMARK 3 4 3.2523 - 2.9550 0.99 2664 135 0.1774 0.2278 REMARK 3 5 2.9550 - 2.7433 1.00 2659 138 0.1846 0.2182 REMARK 3 6 2.7433 - 2.5816 0.99 2630 155 0.1851 0.2051 REMARK 3 7 2.5816 - 2.4523 0.99 2639 125 0.1846 0.2096 REMARK 3 8 2.4523 - 2.3456 0.98 2613 135 0.1904 0.2467 REMARK 3 9 2.3456 - 2.2553 0.99 2609 143 0.1914 0.2226 REMARK 3 10 2.2553 - 2.1775 0.99 2617 135 0.2179 0.2564 REMARK 3 11 2.1775 - 2.1094 0.99 2600 146 0.2185 0.2347 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2408 REMARK 3 ANGLE : 1.430 3271 REMARK 3 CHIRALITY : 0.061 347 REMARK 3 PLANARITY : 0.007 423 REMARK 3 DIHEDRAL : 17.708 869 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN C AND RESSEQ 10:151) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6047 73.3697 -2.5077 REMARK 3 T TENSOR REMARK 3 T11: 0.2138 T22: 0.7188 REMARK 3 T33: 0.2999 T12: -0.0147 REMARK 3 T13: -0.0327 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 3.1131 L22: 3.3575 REMARK 3 L33: 2.6638 L12: -0.6440 REMARK 3 L13: -0.1118 L23: 0.2547 REMARK 3 S TENSOR REMARK 3 S11: -0.0716 S12: -0.7625 S13: 0.1745 REMARK 3 S21: 0.4101 S22: -0.0454 S23: -0.0493 REMARK 3 S31: -0.1994 S32: 0.1815 S33: 0.1078 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 10:152) REMARK 3 ORIGIN FOR THE GROUP (A): 36.0717 63.9842 -7.1982 REMARK 3 T TENSOR REMARK 3 T11: 0.2133 T22: 0.3297 REMARK 3 T33: 0.2124 T12: 0.0850 REMARK 3 T13: -0.0292 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 2.2738 L22: 3.8615 REMARK 3 L33: 4.2026 L12: 0.4416 REMARK 3 L13: -0.3208 L23: 0.0353 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.4216 S13: 0.1201 REMARK 3 S21: 0.5034 S22: 0.0597 S23: -0.0489 REMARK 3 S31: 0.2578 S32: 0.0240 S33: -0.0326 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4P5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31129 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.109 REMARK 200 RESOLUTION RANGE LOW (A) : 38.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 10.2.31 REMARK 200 STARTING MODEL: 4FYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M LITHIUM SULFATE, 1% PEG2K, 20 MM REMARK 280 MAGNESIUM SULFATE, 100 MM TRIS, PH 8.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 18.97400 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 37.94800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.46100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.43500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.48700 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 18.97400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 37.94800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 47.43500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 28.46100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 9.48700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -28.46100 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -37.94800 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION. 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 MET C 8 REMARK 465 ARG C 9 REMARK 465 VAL C 152 REMARK 465 GLU C 153 REMARK 465 HIS C 154 REMARK 465 HIS C 155 REMARK 465 HIS C 156 REMARK 465 HIS C 157 REMARK 465 HIS C 158 REMARK 465 HIS C 159 REMARK 465 MET A 8 REMARK 465 GLU A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 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 O2 SO4 A 202 O HOH A 382 2.12 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 309 O HOH A 309 10664 1.88 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 C 53 C - N - CA ANGL. DEV. = 19.2 DEGREES REMARK 500 PRO C 53 C - N - CD ANGL. DEV. = -16.4 DEGREES REMARK 500 LEU C 151 CA - CB - CG ANGL. DEV. = 20.9 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 ILE C 18 -74.23 -121.86 REMARK 500 LEU C 54 -4.57 86.72 REMARK 500 GLU C 56 7.66 88.89 REMARK 500 GLU C 57 -154.66 -74.67 REMARK 500 ALA C 58 -9.73 96.03 REMARK 500 ALA C 59 -15.58 61.50 REMARK 500 SER C 127 -79.13 -125.77 REMARK 500 ILE A 18 -76.16 -122.05 REMARK 500 PRO A 53 169.04 -49.58 REMARK 500 LEU A 54 -1.27 88.78 REMARK 500 ALA A 58 69.60 66.21 REMARK 500 SER A 127 -79.34 -125.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 52 PRO A 53 -124.56 REMARK 500 GLU A 57 ALA A 58 -119.67 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 N6P C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N6P A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FYI RELATED DB: PDB DBREF 4P5D C 11 151 UNP O35820 DNPH1_RAT 11 151 DBREF 4P5D A 11 151 UNP O35820 DNPH1_RAT 11 151 SEQADV 4P5D MET C 8 UNP O35820 INITIATING METHIONINE SEQADV 4P5D ARG C 9 UNP O35820 EXPRESSION TAG SEQADV 4P5D ARG C 10 UNP O35820 EXPRESSION TAG SEQADV 4P5D ASN C 69 UNP O35820 ASP 69 ENGINEERED MUTATION SEQADV 4P5D VAL C 152 UNP O35820 EXPRESSION TAG SEQADV 4P5D GLU C 153 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 154 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 155 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 156 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 157 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 158 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS C 159 UNP O35820 EXPRESSION TAG SEQADV 4P5D MET A 8 UNP O35820 INITIATING METHIONINE SEQADV 4P5D ARG A 9 UNP O35820 EXPRESSION TAG SEQADV 4P5D ARG A 10 UNP O35820 EXPRESSION TAG SEQADV 4P5D ASN A 69 UNP O35820 ASP 69 ENGINEERED MUTATION SEQADV 4P5D VAL A 152 UNP O35820 EXPRESSION TAG SEQADV 4P5D GLU A 153 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 154 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 155 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 156 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 157 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 158 UNP O35820 EXPRESSION TAG SEQADV 4P5D HIS A 159 UNP O35820 EXPRESSION TAG SEQRES 1 C 152 MET ARG ARG SER VAL TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 C 152 GLY ARG GLU ASP GLN ALA LEU TYR ALA ARG ILE VAL SER SEQRES 3 C 152 ARG LEU ARG ARG TYR GLY LYS VAL LEU THR GLU HIS VAL SEQRES 4 C 152 ALA ASP ALA GLU LEU GLU PRO LEU GLY GLU GLU ALA ALA SEQRES 5 C 152 GLY GLY ASP GLN PHE ILE HIS GLU GLN ASN LEU ASN TRP SEQRES 6 C 152 LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR GLN SEQRES 7 C 152 PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA VAL SEQRES 8 C 152 ALA LEU GLY LYS PRO ILE LEU CYS LEU PHE ARG PRO GLN SEQRES 9 C 152 SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA ALA SEQRES 10 C 152 ASP GLY SER ARG PHE GLN VAL TRP ASP TYR ALA GLU GLY SEQRES 11 C 152 GLU VAL GLU THR MET LEU ASP ARG TYR PHE GLU ALA TYR SEQRES 12 C 152 LEU VAL GLU HIS HIS HIS HIS HIS HIS SEQRES 1 A 152 MET ARG ARG SER VAL TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 A 152 GLY ARG GLU ASP GLN ALA LEU TYR ALA ARG ILE VAL SER SEQRES 3 A 152 ARG LEU ARG ARG TYR GLY LYS VAL LEU THR GLU HIS VAL SEQRES 4 A 152 ALA ASP ALA GLU LEU GLU PRO LEU GLY GLU GLU ALA ALA SEQRES 5 A 152 GLY GLY ASP GLN PHE ILE HIS GLU GLN ASN LEU ASN TRP SEQRES 6 A 152 LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR GLN SEQRES 7 A 152 PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA VAL SEQRES 8 A 152 ALA LEU GLY LYS PRO ILE LEU CYS LEU PHE ARG PRO GLN SEQRES 9 A 152 SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA ALA SEQRES 10 A 152 ASP GLY SER ARG PHE GLN VAL TRP ASP TYR ALA GLU GLY SEQRES 11 A 152 GLU VAL GLU THR MET LEU ASP ARG TYR PHE GLU ALA TYR SEQRES 12 A 152 LEU VAL GLU HIS HIS HIS HIS HIS HIS HET N6P C 201 32 HET N6P A 201 32 HET SO4 A 202 5 HETNAM N6P 6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D- HETNAM 2 N6P RIBOFURANOSYL)-9H-PURINE HETNAM SO4 SULFATE ION HETSYN N6P 6-NAPHTHYLPURINE RIBOSIDE 5'-MONOPHOSPHATE FORMUL 3 N6P 2(C20 H19 N4 O7 P) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *144(H2 O) HELIX 1 AA1 ASP C 24 ARG C 36 1 13 HELIX 2 AA2 THR C 43 ASP C 48 5 6 HELIX 3 AA3 GLY C 60 ALA C 76 1 17 HELIX 4 AA4 SER C 87 GLY C 101 1 15 HELIX 5 AA5 ARG C 109 GLY C 113 5 5 HELIX 6 AA6 SER C 117 GLY C 122 1 6 HELIX 7 AA7 ALA C 135 GLY C 137 5 3 HELIX 8 AA8 GLU C 138 TYR C 150 1 13 HELIX 9 AA9 ASP A 24 ARG A 36 1 13 HELIX 10 AB1 THR A 43 ASP A 48 5 6 HELIX 11 AB2 GLY A 60 ALA A 76 1 17 HELIX 12 AB3 SER A 87 LEU A 100 1 14 HELIX 13 AB4 ARG A 109 GLY A 113 5 5 HELIX 14 AB5 SER A 117 GLY A 122 1 6 HELIX 15 AB6 ALA A 135 GLY A 137 5 3 HELIX 16 AB7 GLU A 138 TYR A 150 1 13 SHEET 1 AA1 5 LYS C 40 VAL C 41 0 SHEET 2 AA1 5 SER C 11 CYS C 15 1 N VAL C 12 O LYS C 40 SHEET 3 AA1 5 VAL C 78 GLU C 82 1 O VAL C 80 N TYR C 13 SHEET 4 AA1 5 ILE C 104 PHE C 108 1 O LEU C 105 N ALA C 81 SHEET 5 AA1 5 PHE C 129 ASP C 133 1 O TRP C 132 N CYS C 106 SHEET 1 AA2 5 LYS A 40 VAL A 41 0 SHEET 2 AA2 5 SER A 11 CYS A 15 1 N VAL A 12 O LYS A 40 SHEET 3 AA2 5 VAL A 78 GLU A 82 1 O VAL A 80 N CYS A 15 SHEET 4 AA2 5 ILE A 104 PHE A 108 1 O LEU A 107 N ALA A 81 SHEET 5 AA2 5 PHE A 129 ASP A 133 1 O TRP A 132 N CYS A 106 SITE 1 AC1 21 TYR C 13 CYS C 15 GLY C 16 SER C 17 SITE 2 AC1 21 ILE C 18 ARG C 19 GLY C 20 HIS C 45 SITE 3 AC1 21 GLU C 57 ALA C 58 ILE C 65 ASN C 69 SITE 4 AC1 21 SER C 87 GLY C 89 GLU C 93 SER C 117 SITE 5 AC1 21 MET C 119 HOH C 304 HOH C 306 HOH C 330 SITE 6 AC1 21 HOH C 344 SITE 1 AC2 23 TYR A 13 CYS A 15 GLY A 16 SER A 17 SITE 2 AC2 23 ILE A 18 ARG A 19 GLY A 20 HIS A 45 SITE 3 AC2 23 VAL A 46 GLU A 57 ALA A 58 ILE A 65 SITE 4 AC2 23 ASN A 69 SER A 87 GLY A 89 VAL A 90 SITE 5 AC2 23 GLU A 93 SER A 117 MET A 119 HOH A 305 SITE 6 AC2 23 HOH A 315 HOH A 369 HOH A 385 SITE 1 AC3 6 ARG A 34 ARG A 36 ARG A 37 HOH A 304 SITE 2 AC3 6 HOH A 317 HOH A 382 CRYST1 178.200 178.200 56.922 90.00 90.00 120.00 P 61 2 2 24 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 0.005612 0.003240 0.000000 0.00000 SCALE2 0.000000 0.006480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017568 0.00000