HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-OCT-21 7SFG TITLE HUMAN DNMT1(729-1600) BOUND TO ZEBULARINE-CONTAINING 12MER DSDNA AND TITLE 2 COFACTOR SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE COMPND 5 HSAI,M.HSAI,MCMT; COMPND 6 EC: 2.1.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA STRAND 1; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA STRAND 2; COMPND 14 CHAIN: D; COMPND 15 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: DNMT1, AIM, CXXC9, DNMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS EPIGENTICS, DNA METHYTRANSFERASE FOLD, MAINTENANCE METHYLATION, KEYWDS 2 INHIBITION, DNA BINDING PROTEIN, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,S.PATHURI,X.CHENG REVDAT 4 18-OCT-23 7SFG 1 REMARK REVDAT 3 15-JUN-22 7SFG 1 JRNL REVDAT 2 20-APR-22 7SFG 1 JRNL REVDAT 1 30-MAR-22 7SFG 0 JRNL AUTH J.R.HORTON,S.PATHURI,K.WONG,R.REN,L.RUEDA,D.T.FOSBENNER, JRNL AUTH 2 D.A.HEERDING,M.T.MCCABE,M.B.PAPPALARDI,X.ZHANG,B.W.KING, JRNL AUTH 3 X.CHENG JRNL TITL STRUCTURAL CHARACTERIZATION OF DICYANOPYRIDINE CONTAINING JRNL TITL 2 DNMT1-SELECTIVE, NON-NUCLEOSIDE INHIBITORS. JRNL REF STRUCTURE V. 30 793 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 35395178 JRNL DOI 10.1016/J.STR.2022.03.009 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 43221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 41.8500 - 5.8600 0.99 3089 149 0.1596 0.1753 REMARK 3 2 5.8600 - 4.6500 1.00 3027 148 0.1543 0.1901 REMARK 3 3 4.6500 - 4.0600 1.00 3004 146 0.1398 0.2029 REMARK 3 4 4.0600 - 3.6900 1.00 3017 146 0.1637 0.1805 REMARK 3 5 3.6900 - 3.4300 0.99 2976 144 0.1760 0.2321 REMARK 3 6 3.4300 - 3.2300 0.99 2988 145 0.1868 0.2544 REMARK 3 7 3.2300 - 3.0700 1.00 3004 146 0.1964 0.2333 REMARK 3 8 3.0600 - 2.9300 1.00 3026 147 0.2074 0.2544 REMARK 3 9 2.9300 - 2.8200 1.00 2986 145 0.2162 0.2738 REMARK 3 10 2.8200 - 2.7200 1.00 2958 143 0.2132 0.2324 REMARK 3 11 2.7200 - 2.6400 1.00 2996 146 0.2196 0.2918 REMARK 3 12 2.6400 - 2.5600 0.99 2989 145 0.2399 0.3088 REMARK 3 13 2.5600 - 2.4900 0.98 2940 142 0.2510 0.3260 REMARK 3 14 2.4900 - 2.4300 0.74 2221 108 0.2719 0.3217 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) : 0.278 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.987 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.61 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 : 0.005 7058 REMARK 3 ANGLE : 0.769 9683 REMARK 3 CHIRALITY : 0.047 1044 REMARK 3 PLANARITY : 0.008 1179 REMARK 3 DIHEDRAL : 17.168 2564 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 730 THROUGH 893 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.9439 -8.8088 17.5716 REMARK 3 T TENSOR REMARK 3 T11: 0.5355 T22: 0.7078 REMARK 3 T33: 0.5767 T12: -0.2581 REMARK 3 T13: -0.1387 T23: 0.1219 REMARK 3 L TENSOR REMARK 3 L11: 4.6209 L22: 1.6800 REMARK 3 L33: 2.2351 L12: 0.8733 REMARK 3 L13: 1.9529 L23: 1.3480 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: 0.0381 S13: 0.0134 REMARK 3 S21: -0.2669 S22: 0.0547 S23: 0.6778 REMARK 3 S31: 0.4677 S32: -0.7694 S33: -0.0915 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 894 THROUGH 1246 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0661 16.6071 24.3077 REMARK 3 T TENSOR REMARK 3 T11: 0.3151 T22: 0.2846 REMARK 3 T33: 0.2554 T12: 0.0824 REMARK 3 T13: 0.0033 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 2.1790 L22: 0.6313 REMARK 3 L33: 1.2130 L12: -0.3667 REMARK 3 L13: 0.6366 L23: 0.0172 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: 0.2649 S13: 0.3013 REMARK 3 S21: -0.0745 S22: -0.0412 S23: -0.0798 REMARK 3 S31: -0.1074 S32: -0.0758 S33: 0.0357 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1247 THROUGH 1600 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6060 4.8881 23.0910 REMARK 3 T TENSOR REMARK 3 T11: 0.2997 T22: 0.3035 REMARK 3 T33: 0.2261 T12: 0.1056 REMARK 3 T13: -0.0345 T23: -0.1296 REMARK 3 L TENSOR REMARK 3 L11: 2.1352 L22: 0.9773 REMARK 3 L33: 1.8076 L12: 0.7152 REMARK 3 L13: 0.9032 L23: 0.0792 REMARK 3 S TENSOR REMARK 3 S11: 0.0639 S12: 0.5154 S13: -0.2311 REMARK 3 S21: -0.0251 S22: 0.2218 S23: -0.1554 REMARK 3 S31: 0.1730 S32: 0.3240 S33: -0.1023 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8671 -7.5833 16.8543 REMARK 3 T TENSOR REMARK 3 T11: 1.0114 T22: 0.5809 REMARK 3 T33: 0.7557 T12: 0.2871 REMARK 3 T13: -0.3175 T23: -0.2389 REMARK 3 L TENSOR REMARK 3 L11: 4.4356 L22: 5.6445 REMARK 3 L33: 6.2368 L12: 0.3475 REMARK 3 L13: -1.0174 L23: -0.3147 REMARK 3 S TENSOR REMARK 3 S11: -0.1929 S12: 0.3748 S13: -0.0152 REMARK 3 S21: 0.0347 S22: 0.7936 S23: 0.0861 REMARK 3 S31: 0.6027 S32: 0.1229 S33: -0.4823 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 13 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6786 -6.7973 18.1078 REMARK 3 T TENSOR REMARK 3 T11: 0.7506 T22: 0.8536 REMARK 3 T33: 0.6349 T12: 0.3798 REMARK 3 T13: -0.1810 T23: -0.3354 REMARK 3 L TENSOR REMARK 3 L11: 3.1637 L22: 3.2302 REMARK 3 L33: 1.0660 L12: 0.1772 REMARK 3 L13: -1.8270 L23: -0.1813 REMARK 3 S TENSOR REMARK 3 S11: 0.2118 S12: 0.8753 S13: -0.5452 REMARK 3 S21: -0.4304 S22: 0.0488 S23: -0.3768 REMARK 3 S31: 0.6396 S32: 0.7279 S33: 0.0181 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 7SFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1000260102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43229 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 41.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6X9I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-18% POLYETHYLENE GLYCOL (PEG) 3350, REMARK 280 0.1 M CITRIC ACID (PH 5.1), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 80.88800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.73800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 80.88800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.73800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 APPLY THE FOLLOWING TO CHAINS: A, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 727 REMARK 465 MET A 728 REMARK 465 ASN A 729 REMARK 465 PRO A 851 REMARK 465 GLU A 852 REMARK 465 SER A 853 REMARK 465 LEU A 854 REMARK 465 LEU A 855 REMARK 465 GLU A 856 REMARK 465 GLY A 857 REMARK 465 ASP A 858 REMARK 465 ASP A 859 REMARK 465 GLY A 860 REMARK 465 THR A 885 REMARK 465 GLU A 886 REMARK 465 ASP A 887 REMARK 465 LEU A 952 REMARK 465 SER A 953 REMARK 465 SER A 954 REMARK 465 PRO A 955 REMARK 465 VAL A 956 REMARK 465 LYS A 957 REMARK 465 ARG A 958 REMARK 465 PRO A 959 REMARK 465 ARG A 960 REMARK 465 LYS A 961 REMARK 465 GLU A 962 REMARK 465 SER A 1105 REMARK 465 PRO A 1106 REMARK 465 GLY A 1107 REMARK 465 ASN A 1108 REMARK 465 LYS A 1109 REMARK 465 GLY A 1110 REMARK 465 LYS A 1111 REMARK 465 GLY A 1112 REMARK 465 LYS A 1113 REMARK 465 GLY A 1114 REMARK 465 LYS A 1115 REMARK 465 GLY A 1116 REMARK 465 LYS A 1117 REMARK 465 GLY A 1118 REMARK 465 LYS A 1119 REMARK 465 PRO A 1120 REMARK 465 LYS A 1121 REMARK 465 SER A 1122 REMARK 465 GLN A 1123 REMARK 465 ALA A 1124 REMARK 465 CYS A 1125 REMARK 465 GLU A 1126 REMARK 465 PRO A 1127 REMARK 465 SER A 1128 REMARK 465 GLU A 1129 REMARK 465 PRO A 1130 REMARK 465 GLU A 1131 REMARK 465 ILE A 1132 REMARK 465 GLU A 1133 REMARK 465 ILE A 1134 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 SER A 732 OG REMARK 470 GLU A 736 CG CD OE1 OE2 REMARK 470 VAL A 738 CG1 CG2 REMARK 470 LYS A 739 CG CD CE NZ REMARK 470 LYS A 743 CG CD CE NZ REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 SER A 745 OG REMARK 470 LYS A 748 CG CD CE NZ REMARK 470 GLU A 755 CG CD OE1 OE2 REMARK 470 LEU A 757 CG CD1 CD2 REMARK 470 ILE A 766 CG1 CG2 CD1 REMARK 470 ASP A 768 CG OD1 OD2 REMARK 470 ASP A 769 CG OD1 OD2 REMARK 470 LYS A 772 CG CD CE NZ REMARK 470 LYS A 831 CG CD CE NZ REMARK 470 ILE A 835 CG1 CG2 CD1 REMARK 470 GLU A 841 CG CD OE1 OE2 REMARK 470 ASP A 850 CG OD1 OD2 REMARK 470 LYS A 861 CG CD CE NZ REMARK 470 LYS A 881 CG CD CE NZ REMARK 470 GLN A 883 CG CD OE1 NE2 REMARK 470 ASN A 888 CG OD1 ND2 REMARK 470 LYS A 889 CG CD CE NZ REMARK 470 PHE A 890 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 891 CG CD CE NZ REMARK 470 GLU A 901 CG CD OE1 OE2 REMARK 470 ARG A 903 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 904 CG CD OE1 NE2 REMARK 470 GLU A 906 CG CD OE1 OE2 REMARK 470 GLU A 912 CG CD OE1 OE2 REMARK 470 GLU A 915 CG CD OE1 OE2 REMARK 470 LYS A 951 CG CD CE NZ REMARK 470 ASP A 967 CG OD1 OD2 REMARK 470 ASP A 978 CG OD1 OD2 REMARK 470 LYS A1003 CG CD CE NZ REMARK 470 LYS A1004 CG CD CE NZ REMARK 470 SER A1005 OG REMARK 470 LYS A1054 CG CD CE NZ REMARK 470 LEU A1068 CG CD1 CD2 REMARK 470 GLU A1070 CG CD OE1 OE2 REMARK 470 LYS A1092 CG CD CE NZ REMARK 470 SER A1095 OG REMARK 470 GLU A1097 CG CD OE1 OE2 REMARK 470 ASP A1098 CG OD1 OD2 REMARK 470 ASN A1101 CG OD1 ND2 REMARK 470 ARG A1104 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1135 CG CD CE NZ REMARK 470 LYS A1244 CG CD CE NZ REMARK 470 LYS A1323 CG CD CE NZ REMARK 470 ARG A1337 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1348 CG CD CE NZ REMARK 470 ARG A1426 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1453 CG CD NE CZ NH1 NH2 REMARK 470 ASP A1461 CG OD1 OD2 REMARK 470 ARG A1462 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1463 CG CD CE NZ REMARK 470 LEU A1472 CG CD1 CD2 REMARK 470 GLU A1480 CG CD OE1 OE2 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 SG CYS A 1226 C5 PYO D 18 2.13 REMARK 500 O HOH A 2021 O HOH A 2047 2.18 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 ASP A 741 -113.23 -95.13 REMARK 500 ASP A 753 -102.78 57.54 REMARK 500 SER A 770 -7.76 -58.54 REMARK 500 SER A 787 -52.58 -132.13 REMARK 500 ASP A 818 58.39 -93.01 REMARK 500 LYS A 889 77.86 63.22 REMARK 500 LEU A 911 -99.40 -114.23 REMARK 500 GLN A 913 -177.52 -66.87 REMARK 500 LEU A 914 -79.77 -152.11 REMARK 500 TYR A 969 77.04 -112.43 REMARK 500 GLU A 971 3.44 -62.69 REMARK 500 SER A1030 -153.70 59.06 REMARK 500 GLU A1070 153.41 67.86 REMARK 500 TYR A1240 110.53 -168.49 REMARK 500 SER A1241 34.61 -152.04 REMARK 500 ASP A1347 -14.04 70.64 REMARK 500 MET A1371 17.49 -156.71 REMARK 500 ALA A1481 -154.39 52.54 REMARK 500 GLU A1543 -45.47 -132.18 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 ZN A1702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 793 NE2 REMARK 620 2 CYS A 820 SG 117.2 REMARK 620 3 CYS A 893 SG 100.0 116.7 REMARK 620 4 CYS A 896 SG 94.1 115.8 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1476 SG REMARK 620 2 CYS A1478 SG 81.5 REMARK 620 3 CYS A1485 SG 132.0 138.5 REMARK 620 4 HIS A1502 NE2 95.8 86.6 108.9 REMARK 620 N 1 2 3 DBREF 7SFG A 729 1600 UNP P26358 DNMT1_HUMAN 393 1264 DBREF 7SFG C 1 12 PDB 7SFG 7SFG 1 12 DBREF 7SFG D 13 24 PDB 7SFG 7SFG 13 24 SEQADV 7SFG HIS A 727 UNP P26358 EXPRESSION TAG SEQADV 7SFG MET A 728 UNP P26358 EXPRESSION TAG SEQRES 1 A 874 HIS MET ASN ARG ILE SER TRP VAL GLY GLU ALA VAL LYS SEQRES 2 A 874 THR ASP GLY LYS LYS SER TYR TYR LYS LYS VAL CYS ILE SEQRES 3 A 874 ASP ALA GLU THR LEU GLU VAL GLY ASP CYS VAL SER VAL SEQRES 4 A 874 ILE PRO ASP ASP SER SER LYS PRO LEU TYR LEU ALA ARG SEQRES 5 A 874 VAL THR ALA LEU TRP GLU ASP SER SER ASN GLY GLN MET SEQRES 6 A 874 PHE HIS ALA HIS TRP PHE CYS ALA GLY THR ASP THR VAL SEQRES 7 A 874 LEU GLY ALA THR SER ASP PRO LEU GLU LEU PHE LEU VAL SEQRES 8 A 874 ASP GLU CYS GLU ASP MET GLN LEU SER TYR ILE HIS SER SEQRES 9 A 874 LYS VAL LYS VAL ILE TYR LYS ALA PRO SER GLU ASN TRP SEQRES 10 A 874 ALA MET GLU GLY GLY MET ASP PRO GLU SER LEU LEU GLU SEQRES 11 A 874 GLY ASP ASP GLY LYS THR TYR PHE TYR GLN LEU TRP TYR SEQRES 12 A 874 ASP GLN ASP TYR ALA ARG PHE GLU SER PRO PRO LYS THR SEQRES 13 A 874 GLN PRO THR GLU ASP ASN LYS PHE LYS PHE CYS VAL SER SEQRES 14 A 874 CYS ALA ARG LEU ALA GLU MET ARG GLN LYS GLU ILE PRO SEQRES 15 A 874 ARG VAL LEU GLU GLN LEU GLU ASP LEU ASP SER ARG VAL SEQRES 16 A 874 LEU TYR TYR SER ALA THR LYS ASN GLY ILE LEU TYR ARG SEQRES 17 A 874 VAL GLY ASP GLY VAL TYR LEU PRO PRO GLU ALA PHE THR SEQRES 18 A 874 PHE ASN ILE LYS LEU SER SER PRO VAL LYS ARG PRO ARG SEQRES 19 A 874 LYS GLU PRO VAL ASP GLU ASP LEU TYR PRO GLU HIS TYR SEQRES 20 A 874 ARG LYS TYR SER ASP TYR ILE LYS GLY SER ASN LEU ASP SEQRES 21 A 874 ALA PRO GLU PRO TYR ARG ILE GLY ARG ILE LYS GLU ILE SEQRES 22 A 874 PHE CYS PRO LYS LYS SER ASN GLY ARG PRO ASN GLU THR SEQRES 23 A 874 ASP ILE LYS ILE ARG VAL ASN LYS PHE TYR ARG PRO GLU SEQRES 24 A 874 ASN THR HIS LYS SER THR PRO ALA SER TYR HIS ALA ASP SEQRES 25 A 874 ILE ASN LEU LEU TYR TRP SER ASP GLU GLU ALA VAL VAL SEQRES 26 A 874 ASP PHE LYS ALA VAL GLN GLY ARG CYS THR VAL GLU TYR SEQRES 27 A 874 GLY GLU ASP LEU PRO GLU CYS VAL GLN VAL TYR SER MET SEQRES 28 A 874 GLY GLY PRO ASN ARG PHE TYR PHE LEU GLU ALA TYR ASN SEQRES 29 A 874 ALA LYS SER LYS SER PHE GLU ASP PRO PRO ASN HIS ALA SEQRES 30 A 874 ARG SER PRO GLY ASN LYS GLY LYS GLY LYS GLY LYS GLY SEQRES 31 A 874 LYS GLY LYS PRO LYS SER GLN ALA CYS GLU PRO SER GLU SEQRES 32 A 874 PRO GLU ILE GLU ILE LYS LEU PRO LYS LEU ARG THR LEU SEQRES 33 A 874 ASP VAL PHE SER GLY CYS GLY GLY LEU SER GLU GLY PHE SEQRES 34 A 874 HIS GLN ALA GLY ILE SER ASP THR LEU TRP ALA ILE GLU SEQRES 35 A 874 MET TRP ASP PRO ALA ALA GLN ALA PHE ARG LEU ASN ASN SEQRES 36 A 874 PRO GLY SER THR VAL PHE THR GLU ASP CYS ASN ILE LEU SEQRES 37 A 874 LEU LYS LEU VAL MET ALA GLY GLU THR THR ASN SER ARG SEQRES 38 A 874 GLY GLN ARG LEU PRO GLN LYS GLY ASP VAL GLU MET LEU SEQRES 39 A 874 CYS GLY GLY PRO PRO CYS GLN GLY PHE SER GLY MET ASN SEQRES 40 A 874 ARG PHE ASN SER ARG THR TYR SER LYS PHE LYS ASN SER SEQRES 41 A 874 LEU VAL VAL SER PHE LEU SER TYR CYS ASP TYR TYR ARG SEQRES 42 A 874 PRO ARG PHE PHE LEU LEU GLU ASN VAL ARG ASN PHE VAL SEQRES 43 A 874 SER PHE LYS ARG SER MET VAL LEU LYS LEU THR LEU ARG SEQRES 44 A 874 CYS LEU VAL ARG MET GLY TYR GLN CYS THR PHE GLY VAL SEQRES 45 A 874 LEU GLN ALA GLY GLN TYR GLY VAL ALA GLN THR ARG ARG SEQRES 46 A 874 ARG ALA ILE ILE LEU ALA ALA ALA PRO GLY GLU LYS LEU SEQRES 47 A 874 PRO LEU PHE PRO GLU PRO LEU HIS VAL PHE ALA PRO ARG SEQRES 48 A 874 ALA CYS GLN LEU SER VAL VAL VAL ASP ASP LYS LYS PHE SEQRES 49 A 874 VAL SER ASN ILE THR ARG LEU SER SER GLY PRO PHE ARG SEQRES 50 A 874 THR ILE THR VAL ARG ASP THR MET SER ASP LEU PRO GLU SEQRES 51 A 874 VAL ARG ASN GLY ALA SER ALA LEU GLU ILE SER TYR ASN SEQRES 52 A 874 GLY GLU PRO GLN SER TRP PHE GLN ARG GLN LEU ARG GLY SEQRES 53 A 874 ALA GLN TYR GLN PRO ILE LEU ARG ASP HIS ILE CYS LYS SEQRES 54 A 874 ASP MET SER ALA LEU VAL ALA ALA ARG MET ARG HIS ILE SEQRES 55 A 874 PRO LEU ALA PRO GLY SER ASP TRP ARG ASP LEU PRO ASN SEQRES 56 A 874 ILE GLU VAL ARG LEU SER ASP GLY THR MET ALA ARG LYS SEQRES 57 A 874 LEU ARG TYR THR HIS HIS ASP ARG LYS ASN GLY ARG SER SEQRES 58 A 874 SER SER GLY ALA LEU ARG GLY VAL CYS SER CYS VAL GLU SEQRES 59 A 874 ALA GLY LYS ALA CYS ASP PRO ALA ALA ARG GLN PHE ASN SEQRES 60 A 874 THR LEU ILE PRO TRP CYS LEU PRO HIS THR GLY ASN ARG SEQRES 61 A 874 HIS ASN HIS TRP ALA GLY LEU TYR GLY ARG LEU GLU TRP SEQRES 62 A 874 ASP GLY PHE PHE SER THR THR VAL THR ASN PRO GLU PRO SEQRES 63 A 874 MET GLY LYS GLN GLY ARG VAL LEU HIS PRO GLU GLN HIS SEQRES 64 A 874 ARG VAL VAL SER VAL ARG GLU CYS ALA ARG SER GLN GLY SEQRES 65 A 874 PHE PRO ASP THR TYR ARG LEU PHE GLY ASN ILE LEU ASP SEQRES 66 A 874 LYS HIS ARG GLN VAL GLY ASN ALA VAL PRO PRO PRO LEU SEQRES 67 A 874 ALA LYS ALA ILE GLY LEU GLU ILE LYS LEU CYS MET LEU SEQRES 68 A 874 ALA LYS ALA SEQRES 1 C 12 DG DA DG DG DC 5CM DG DC DC DT DG DC SEQRES 1 D 12 DG DC DA DG DG PYO DG DG DC DC DT DC HET 5CM C 6 20 HET PYO D 18 19 HET ZN A1701 1 HET ZN A1702 1 HET SAM A1703 27 HET GOL A1704 6 HET EDO A1705 4 HET EDO A1706 4 HET EDO A1707 4 HET EDO A1708 4 HET EDO A1709 4 HET EDO A1710 4 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM PYO 1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5'-PHOSPHATE HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 3 PYO C9 H13 N2 O8 P FORMUL 4 ZN 2(ZN 2+) FORMUL 6 SAM C15 H22 N6 O5 S FORMUL 7 GOL C3 H8 O3 FORMUL 8 EDO 6(C2 H6 O2) FORMUL 14 HOH *287(H2 O) HELIX 1 AA1 THR A 801 THR A 803 5 3 HELIX 2 AA2 LEU A 805 SER A 809 5 5 HELIX 3 AA3 ASN A 842 GLU A 846 5 5 HELIX 4 AA4 CYS A 893 ILE A 907 1 15 HELIX 5 AA5 TYR A 969 TYR A 976 5 8 HELIX 6 AA6 ARG A 1023 THR A 1027 5 5 HELIX 7 AA7 SER A 1030 TYR A 1035 5 6 HELIX 8 AA8 LYS A 1054 VAL A 1056 5 3 HELIX 9 AA9 CYS A 1071 GLY A 1078 1 8 HELIX 10 AB1 PRO A 1100 ARG A 1104 5 5 HELIX 11 AB2 GLY A 1149 ALA A 1158 1 10 HELIX 12 AB3 TRP A 1170 ASN A 1181 1 12 HELIX 13 AB4 ASP A 1190 ALA A 1200 1 11 HELIX 14 AB5 LYS A 1242 ASN A 1245 5 4 HELIX 15 AB6 SER A 1246 ARG A 1259 1 14 HELIX 16 AB7 ASN A 1270 VAL A 1272 5 3 HELIX 17 AB8 SER A 1273 GLY A 1291 1 19 HELIX 18 AB9 GLY A 1302 GLY A 1305 5 4 HELIX 19 AC1 ALA A 1335 GLN A 1340 5 6 HELIX 20 AC2 THR A 1366 SER A 1372 1 7 HELIX 21 AC3 SER A 1394 GLY A 1402 1 9 HELIX 22 AC4 SER A 1418 HIS A 1427 1 10 HELIX 23 AC5 ASP A 1435 LEU A 1439 5 5 HELIX 24 AC6 TRP A 1498 GLY A 1504 1 7 HELIX 25 AC7 ASN A 1505 ALA A 1511 5 7 HELIX 26 AC8 SER A 1549 GLN A 1557 1 9 HELIX 27 AC9 ASN A 1568 ASN A 1578 1 11 HELIX 28 AD1 PRO A 1581 ALA A 1600 1 20 SHEET 1 AA1 3 ILE A 731 VAL A 734 0 SHEET 2 AA1 3 LYS A 749 ILE A 752 -1 O LYS A 749 N VAL A 734 SHEET 3 AA1 3 GLU A 755 GLU A 758 -1 O LEU A 757 N VAL A 750 SHEET 1 AA2 6 LYS A 744 TYR A 747 0 SHEET 2 AA2 6 TYR A 775 ASP A 785 -1 O GLU A 784 N SER A 745 SHEET 3 AA2 6 GLN A 790 ALA A 799 -1 O MET A 791 N TRP A 783 SHEET 4 AA2 6 GLU A 813 GLN A 824 -1 O MET A 823 N PHE A 792 SHEET 5 AA2 6 TYR A 863 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 6 AA2 6 VAL A 834 TYR A 836 1 N ILE A 835 O TYR A 865 SHEET 1 AA314 ILE A 828 VAL A 832 0 SHEET 2 AA314 CYS A 762 VAL A 765 -1 N SER A 764 O HIS A 829 SHEET 3 AA314 TYR A 775 ASP A 785 -1 O TYR A 775 N VAL A 765 SHEET 4 AA314 GLN A 790 ALA A 799 -1 O MET A 791 N TRP A 783 SHEET 5 AA314 GLU A 813 GLN A 824 -1 O MET A 823 N PHE A 792 SHEET 6 AA314 TYR A 863 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 7 AA314 ARG A 875 GLU A 877 -1 O GLU A 877 N TRP A 868 SHEET 8 AA314 GLN A1293 GLN A1300 -1 O CYS A1294 N PHE A 876 SHEET 9 AA314 ARG A1311 ALA A1318 -1 O ILE A1314 N GLY A1297 SHEET 10 AA314 PHE A1262 VAL A1268 -1 N LEU A1265 O ILE A1315 SHEET 11 AA314 MET A1219 GLY A1222 1 N LEU A1220 O PHE A1262 SHEET 12 AA314 LEU A1139 VAL A1144 1 N LEU A1142 O MET A1219 SHEET 13 AA314 SER A1161 ILE A1167 1 O ASP A1162 N THR A1141 SHEET 14 AA314 THR A1185 PHE A1187 1 O PHE A1187 N ALA A1166 SHEET 1 AA4 3 ARG A 909 VAL A 910 0 SHEET 2 AA4 3 SER A 925 LYS A 928 -1 O THR A 927 N ARG A 909 SHEET 3 AA4 3 ILE A 931 ARG A 934 -1 O TYR A 933 N ALA A 926 SHEET 1 AA5 7 GLN A 913 ASP A 916 0 SHEET 2 AA5 7 ARG A 920 TYR A 923 -1 O LEU A 922 N GLU A 915 SHEET 3 AA5 7 ARG A 992 PRO A1002 -1 O ILE A 999 N TYR A 923 SHEET 4 AA5 7 GLY A 938 LEU A 941 -1 N LEU A 941 O ARG A 992 SHEET 5 AA5 7 GLY A1058 TYR A1064 -1 O GLY A1058 N TYR A 940 SHEET 6 AA5 7 ARG A1082 ALA A1088 1 O PHE A1083 N THR A1061 SHEET 7 AA5 7 LEU A1041 TRP A1044 1 N LEU A1042 O TYR A1084 SHEET 1 AA6 5 GLN A 913 ASP A 916 0 SHEET 2 AA6 5 ARG A 920 TYR A 923 -1 O LEU A 922 N GLU A 915 SHEET 3 AA6 5 ARG A 992 PRO A1002 -1 O ILE A 999 N TYR A 923 SHEET 4 AA6 5 LYS A1015 LYS A1020 -1 O ARG A1017 N LYS A 997 SHEET 5 AA6 5 GLU A1048 ASP A1052 -1 O ALA A1049 N VAL A1018 SHEET 1 AA7 2 VAL A1343 VAL A1345 0 SHEET 2 AA7 2 LYS A1348 PHE A1350 -1 O PHE A1350 N VAL A1343 SHEET 1 AA8 2 GLU A1385 ILE A1386 0 SHEET 2 AA8 2 LEU A1409 ARG A1410 -1 O LEU A1409 N ILE A1386 SHEET 1 AA9 2 VAL A1444 ARG A1445 0 SHEET 2 AA9 2 MET A1451 ALA A1452 -1 O ALA A1452 N VAL A1444 LINK SG CYS A1226 C6 PYO D 18 1555 1555 1.77 LINK O3' DC C 5 P 5CM C 6 1555 1555 1.61 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK O3' DG D 17 P PYO D 18 1555 1555 1.61 LINK O3' PYO D 18 P DG D 19 1555 1555 1.60 LINK NE2 HIS A 793 ZN ZN A1702 1555 1555 2.10 LINK SG CYS A 820 ZN ZN A1702 1555 1555 2.28 LINK SG CYS A 893 ZN ZN A1702 1555 1555 2.30 LINK SG CYS A 896 ZN ZN A1702 1555 1555 2.20 LINK SG CYS A1476 ZN ZN A1701 1555 1555 2.26 LINK SG CYS A1478 ZN ZN A1701 1555 1555 2.36 LINK SG CYS A1485 ZN ZN A1701 1555 1555 2.29 LINK NE2 HIS A1502 ZN ZN A1701 1555 1555 2.13 CRYST1 161.776 77.476 116.709 90.00 125.67 90.00 C 1 2 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 0.006181 0.000000 0.004437 0.00000 SCALE2 0.000000 0.012907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010547 0.00000