HEADER HYDROLASE 16-MAR-14 4P5E TITLE CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE- TITLE 2 RIBOSIDE-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: C-MYC-RESPONSIVE PROTEIN RCL; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DNPH1, C6ORF108, 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 RCL, DNPH1, INHIBITOR, ROSSMANN FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PADILLA,G.LABESSE,P.A.KAMINSKI REVDAT 2 20-DEC-23 4P5E 1 LINK REVDAT 1 20-AUG-14 4P5E 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 58476 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2957 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 47.3860 - 3.7240 1.00 2720 148 0.1467 0.1541 REMARK 3 2 3.7240 - 2.9560 1.00 2697 142 0.1360 0.1514 REMARK 3 3 2.9560 - 2.5824 1.00 2658 126 0.1479 0.1704 REMARK 3 4 2.5824 - 2.3463 1.00 2629 168 0.1464 0.1636 REMARK 3 5 2.3463 - 2.1781 1.00 2646 141 0.1433 0.1680 REMARK 3 6 2.1781 - 2.0497 1.00 2674 122 0.1451 0.2038 REMARK 3 7 2.0497 - 1.9470 1.00 2627 138 0.1484 0.1986 REMARK 3 8 1.9470 - 1.8623 1.00 2636 160 0.1542 0.1791 REMARK 3 9 1.8623 - 1.7906 1.00 2662 124 0.1493 0.1628 REMARK 3 10 1.7906 - 1.7288 1.00 2655 144 0.1574 0.2003 REMARK 3 11 1.7288 - 1.6747 1.00 2625 109 0.1633 0.2118 REMARK 3 12 1.6747 - 1.6269 1.00 2651 140 0.1622 0.1978 REMARK 3 13 1.6269 - 1.5840 1.00 2616 148 0.1609 0.1875 REMARK 3 14 1.5840 - 1.5454 1.00 2644 141 0.1640 0.1963 REMARK 3 15 1.5454 - 1.5102 1.00 2608 167 0.1741 0.2142 REMARK 3 16 1.5102 - 1.4781 1.00 2615 149 0.1801 0.2032 REMARK 3 17 1.4781 - 1.4485 1.00 2654 141 0.1841 0.2164 REMARK 3 18 1.4485 - 1.4212 1.00 2632 133 0.2012 0.2396 REMARK 3 19 1.4212 - 1.3958 1.00 2637 118 0.2023 0.2502 REMARK 3 20 1.3958 - 1.3721 1.00 2589 153 0.2272 0.2327 REMARK 3 21 1.3721 - 1.3500 1.00 2644 145 0.2182 0.2599 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.40 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 2473 REMARK 3 ANGLE : 1.311 3357 REMARK 3 CHIRALITY : 0.064 365 REMARK 3 PLANARITY : 0.007 435 REMARK 3 DIHEDRAL : 17.339 937 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 4.3321 -1.1574 8.1076 REMARK 3 T TENSOR REMARK 3 T11: 0.0675 T22: 0.0709 REMARK 3 T33: 0.0534 T12: -0.0038 REMARK 3 T13: -0.0040 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.9301 L22: 1.0640 REMARK 3 L33: 1.0970 L12: -0.1657 REMARK 3 L13: -0.0416 L23: 0.2390 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: 0.1595 S13: -0.1174 REMARK 3 S21: -0.0669 S22: 0.0118 S23: 0.0708 REMARK 3 S31: 0.0607 S32: -0.0625 S33: 0.0220 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -25.7798 10.3905 18.0236 REMARK 3 T TENSOR REMARK 3 T11: 0.0629 T22: 0.0798 REMARK 3 T33: 0.0552 T12: 0.0014 REMARK 3 T13: -0.0064 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.6333 L22: 1.0274 REMARK 3 L33: 1.1990 L12: -0.0068 REMARK 3 L13: 0.2100 L23: 0.2709 REMARK 3 S TENSOR REMARK 3 S11: -0.0267 S12: -0.0965 S13: 0.1104 REMARK 3 S21: 0.0442 S22: 0.0413 S23: -0.0643 REMARK 3 S31: -0.0812 S32: 0.0743 S33: -0.0168 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 4P5E 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_1000200721. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8103 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58489 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 47.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: 4FYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3K, 200 MM CALCIUM ACETATE, 100 REMARK 280 MM TRIS, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.14200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -48.97400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 48.97400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 19 REMARK 465 ALA A 60 REMARK 465 GLU A 61 REMARK 465 LEU A 62 REMARK 465 GLY A 63 REMARK 465 ALA A 64 REMARK 465 ARG A 65 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 MET B 19 REMARK 465 GLY B 63 REMARK 465 ALA B 64 REMARK 465 ARG B 65 REMARK 465 GLY B 66 REMARK 465 GLU B 67 REMARK 465 GLU B 68 REMARK 465 ALA B 69 REMARK 465 ALA B 70 REMARK 465 GLY B 71 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 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 350 O HOH B 364 1.58 REMARK 500 O HOH A 459 O HOH B 380 1.82 REMARK 500 O HOH A 302 O HOH A 327 1.89 REMARK 500 O HOH A 469 O HOH A 471 1.94 REMARK 500 O HOH A 461 O HOH B 463 1.95 REMARK 500 O HOH A 481 O HOH A 483 1.95 REMARK 500 O HOH A 355 O HOH A 457 1.96 REMARK 500 O HOH B 494 O HOH B 502 1.98 REMARK 500 O HOH A 378 O HOH A 463 1.99 REMARK 500 OD1 ASP B 161 O HOH B 301 1.99 REMARK 500 O HOH B 363 O HOH B 503 2.01 REMARK 500 O HOH A 475 O HOH B 495 2.01 REMARK 500 OD1 ASP A 161 O HOH A 464 2.05 REMARK 500 O HOH B 343 O HOH B 365 2.06 REMARK 500 NH1 ARG A 20 O HOH A 301 2.07 REMARK 500 O HOH A 474 O HOH A 480 2.07 REMARK 500 O HOH A 447 O HOH A 455 2.07 REMARK 500 O HOH A 307 O HOH A 325 2.10 REMARK 500 OD2 ASP B 161 O HOH B 497 2.13 REMARK 500 O HOH B 332 O HOH B 371 2.13 REMARK 500 OE2 GLU A 34 O HOH A 302 2.14 REMARK 500 O HOH A 443 O HOH B 488 2.15 REMARK 500 O HOH A 465 O HOH A 468 2.17 REMARK 500 OG SER A 138 O HOH A 303 2.19 REMARK 500 OE2 GLU B 34 O HOH B 302 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 324 O HOH B 382 1655 2.04 REMARK 500 O HOH A 369 O HOH B 363 2545 2.19 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 A 29 -75.30 -120.50 REMARK 500 SER A 128 129.06 -30.32 REMARK 500 SER A 138 -78.40 -128.86 REMARK 500 ILE B 29 -76.23 -121.35 REMARK 500 GLU B 55 5.10 -59.29 REMARK 500 SER B 128 125.78 -27.72 REMARK 500 SER B 138 -75.37 -131.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 79 OE1 REMARK 620 2 ASP B 161 OD1 69.2 REMARK 620 3 PRO B 162 O 66.9 3.0 REMARK 620 4 GLU B 164 OE1 69.2 6.2 4.8 REMARK 620 5 GLU B 164 OE2 70.0 4.8 4.1 1.7 REMARK 620 6 HOH B 349 O 69.6 4.2 3.5 2.1 0.7 REMARK 620 7 HOH B 362 O 71.1 2.1 4.3 5.6 3.9 3.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N6P A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N6P B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FYI RELATED DB: PDB REMARK 900 RELATED ID: 4P5D RELATED DB: PDB DBREF 4P5E A 20 162 UNP O43598 DNPH1_HUMAN 20 162 DBREF 4P5E B 20 162 UNP O43598 DNPH1_HUMAN 20 162 SEQADV 4P5E MET A 19 UNP O43598 INITIATING METHIONINE SEQADV 4P5E LEU A 163 UNP O43598 EXPRESSION TAG SEQADV 4P5E GLU A 164 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 165 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 166 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 167 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 168 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 169 UNP O43598 EXPRESSION TAG SEQADV 4P5E HIS A 170 UNP O43598 EXPRESSION TAG SEQRES 1 A 152 MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 A 152 GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SER SEQRES 3 A 152 ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS VAL SEQRES 4 A 152 ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA ALA SEQRES 5 A 152 GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP LEU GLU 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 PHE ASN LYS ARG 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 GLU GLU GLY SEQRES 11 A 152 GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA ASP SEQRES 12 A 152 PRO LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 152 MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG GLY SEQRES 2 B 152 GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SER SEQRES 3 B 152 ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS VAL SEQRES 4 B 152 ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA ALA SEQRES 5 B 152 GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP LEU GLU TRP SEQRES 6 B 152 LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR GLN SEQRES 7 B 152 PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA VAL SEQRES 8 B 152 ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE ARG PRO GLN SEQRES 9 B 152 SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA ALA SEQRES 10 B 152 ASP GLY SER ARG PHE GLN VAL TRP ASP TYR GLU GLU GLY SEQRES 11 B 152 GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA ASP SEQRES 12 B 152 PRO LEU GLU HIS HIS HIS HIS HIS HIS HET N6P A 201 32 HET N6P B 201 32 HET CA B 202 1 HETNAM N6P 6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D- HETNAM 2 N6P RIBOFURANOSYL)-9H-PURINE HETNAM CA CALCIUM ION HETSYN N6P 6-NAPHTHYLPURINE RIBOSIDE 5'-MONOPHOSPHATE FORMUL 3 N6P 2(C20 H19 N4 O7 P) FORMUL 5 CA CA 2+ FORMUL 6 HOH *387(H2 O) HELIX 1 AA1 ASP A 35 ARG A 47 1 13 HELIX 2 AA2 THR A 54 ALA A 59 5 6 HELIX 3 AA3 GLY A 72 ALA A 87 1 16 HELIX 4 AA4 SER A 98 PHE A 111 1 14 HELIX 5 AA5 ARG A 120 GLY A 124 5 5 HELIX 6 AA6 SER A 128 ALA A 135 1 8 HELIX 7 AA7 GLU A 146 GLY A 148 5 3 HELIX 8 AA8 GLU A 149 ASP A 161 1 13 HELIX 9 AA9 ASP B 35 ARG B 47 1 13 HELIX 10 AB1 ASP B 73 ALA B 87 1 15 HELIX 11 AB2 SER B 98 PHE B 111 1 14 HELIX 12 AB3 ARG B 120 GLY B 124 5 5 HELIX 13 AB4 SER B 128 ALA B 135 1 8 HELIX 14 AB5 GLU B 146 GLY B 148 5 3 HELIX 15 AB6 GLU B 149 ASP B 161 1 13 SHEET 1 AA1 5 THR A 51 VAL A 52 0 SHEET 2 AA1 5 ALA A 22 CYS A 26 1 N LEU A 23 O THR A 51 SHEET 3 AA1 5 VAL A 89 GLU A 93 1 O VAL A 91 N TYR A 24 SHEET 4 AA1 5 ILE A 115 PHE A 119 1 O LEU A 118 N ALA A 92 SHEET 5 AA1 5 PHE A 140 ASP A 144 1 O GLN A 141 N CYS A 117 SHEET 1 AA2 5 THR B 51 VAL B 52 0 SHEET 2 AA2 5 ALA B 22 CYS B 26 1 N LEU B 23 O THR B 51 SHEET 3 AA2 5 VAL B 89 GLU B 93 1 O VAL B 91 N TYR B 24 SHEET 4 AA2 5 ILE B 115 PHE B 119 1 O LEU B 118 N ALA B 92 SHEET 5 AA2 5 PHE B 140 ASP B 144 1 O TRP B 143 N CYS B 117 LINK OE1 GLN A 79 CA CA B 202 1555 2545 2.46 LINK OD1AASP B 161 CA CA B 202 1555 1555 2.59 LINK O PRO B 162 CA CA B 202 1555 1555 2.34 LINK OE1 GLU B 164 CA CA B 202 1555 1555 2.59 LINK OE2 GLU B 164 CA CA B 202 1555 1555 2.76 LINK CA CA B 202 O HOH B 349 1555 1555 2.31 LINK CA CA B 202 O HOH B 362 1555 1555 2.33 SITE 1 AC1 19 CYS A 26 GLY A 27 SER A 28 ILE A 29 SITE 2 AC1 19 ARG A 30 GLY A 31 HIS A 56 VAL A 57 SITE 3 AC1 19 GLU A 67 ILE A 76 ASP A 80 SER A 98 SITE 4 AC1 19 GLY A 100 GLU A 104 HOH A 309 HOH A 323 SITE 5 AC1 19 HOH A 421 SER B 128 MET B 130 SITE 1 AC2 16 SER A 128 MET A 130 CYS B 26 GLY B 27 SITE 2 AC2 16 SER B 28 ILE B 29 ARG B 30 GLY B 31 SITE 3 AC2 16 ILE B 76 ASP B 80 SER B 98 GLY B 100 SITE 4 AC2 16 GLU B 104 HOH B 317 HOH B 336 HOH B 348 SITE 1 AC3 5 ASP B 161 PRO B 162 GLU B 164 HOH B 349 SITE 2 AC3 5 HOH B 362 CRYST1 48.974 52.284 54.454 90.00 104.77 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020419 0.000000 0.005382 0.00000 SCALE2 0.000000 0.019126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018991 0.00000