HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-OCT-21 7SFE TITLE HUMAN DNMT1(729-1600) BOUND TO ZEBULARINE-CONTAINING 12MER DSDNA AND TITLE 2 INHIBITOR GSK3830334A 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 (12-MER); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (12-MER); 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 7SFE 1 REMARK REVDAT 3 15-JUN-22 7SFE 1 JRNL REVDAT 2 20-APR-22 7SFE 1 JRNL REVDAT 1 30-MAR-22 7SFE 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. 2.55 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 38149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1908 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 42.1300 - 6.1500 0.97 2665 140 0.1773 0.1766 REMARK 3 2 6.1500 - 4.8800 0.99 2669 141 0.1777 0.2121 REMARK 3 3 4.8800 - 4.2600 0.99 2634 139 0.1493 0.1969 REMARK 3 4 4.2600 - 3.8700 0.99 2636 138 0.1621 0.2008 REMARK 3 5 3.8700 - 3.6000 0.98 2585 137 0.1993 0.2451 REMARK 3 6 3.6000 - 3.3900 0.99 2630 138 0.2023 0.2490 REMARK 3 7 3.3800 - 3.2200 0.99 2603 136 0.2143 0.2632 REMARK 3 8 3.2200 - 3.0800 0.99 2651 140 0.2435 0.2648 REMARK 3 9 3.0800 - 2.9600 0.99 2617 138 0.2729 0.3233 REMARK 3 10 2.9600 - 2.8600 0.99 2624 138 0.2531 0.2980 REMARK 3 11 2.8600 - 2.7700 0.99 2601 138 0.2585 0.3101 REMARK 3 12 2.7700 - 2.6900 0.98 2580 135 0.2700 0.2785 REMARK 3 13 2.6900 - 2.6200 0.96 2493 131 0.3112 0.3348 REMARK 3 14 2.6200 - 2.5500 0.85 2253 119 0.3777 0.4353 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) : 0.369 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.072 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.23 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 : 0.002 7344 REMARK 3 ANGLE : 0.536 10084 REMARK 3 CHIRALITY : 0.040 1083 REMARK 3 PLANARITY : 0.004 1238 REMARK 3 DIHEDRAL : 14.982 2695 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 730 THROUGH 877 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8044 -11.0456 29.5698 REMARK 3 T TENSOR REMARK 3 T11: 0.5913 T22: 0.5098 REMARK 3 T33: 0.6323 T12: 0.1685 REMARK 3 T13: -0.0728 T23: -0.0768 REMARK 3 L TENSOR REMARK 3 L11: 6.8972 L22: 3.4821 REMARK 3 L33: 4.4261 L12: -1.5701 REMARK 3 L13: 2.9321 L23: -1.4931 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: -0.1821 S13: -0.1838 REMARK 3 S21: 0.1246 S22: -0.0478 S23: -0.8323 REMARK 3 S31: 0.2220 S32: 0.4525 S33: 0.0170 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 878 THROUGH 960 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3339 20.9225 32.9049 REMARK 3 T TENSOR REMARK 3 T11: 0.5028 T22: 0.5732 REMARK 3 T33: 0.4008 T12: -0.1524 REMARK 3 T13: 0.0107 T23: -0.0510 REMARK 3 L TENSOR REMARK 3 L11: 1.4328 L22: 5.5385 REMARK 3 L33: 2.1267 L12: 1.2110 REMARK 3 L13: 1.4279 L23: -0.5567 REMARK 3 S TENSOR REMARK 3 S11: 0.3483 S12: -0.4618 S13: 0.4125 REMARK 3 S21: -0.0288 S22: -0.1902 S23: -0.7521 REMARK 3 S31: 0.0873 S32: 0.3033 S33: -0.1908 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 961 THROUGH 1013 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.3567 19.3211 40.6531 REMARK 3 T TENSOR REMARK 3 T11: 0.5812 T22: 0.7397 REMARK 3 T33: 0.3658 T12: -0.1120 REMARK 3 T13: 0.0450 T23: -0.0706 REMARK 3 L TENSOR REMARK 3 L11: 8.1548 L22: 2.1122 REMARK 3 L33: 0.0807 L12: 3.1649 REMARK 3 L13: -0.1437 L23: -0.3254 REMARK 3 S TENSOR REMARK 3 S11: 0.2510 S12: -1.5525 S13: 0.1594 REMARK 3 S21: 0.3109 S22: -0.3189 S23: -0.0047 REMARK 3 S31: -0.1575 S32: 0.0062 S33: 0.0468 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1014 THROUGH 1600 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.9840 7.1310 21.3296 REMARK 3 T TENSOR REMARK 3 T11: 0.3686 T22: 0.2932 REMARK 3 T33: 0.2544 T12: -0.0422 REMARK 3 T13: -0.0281 T23: 0.0600 REMARK 3 L TENSOR REMARK 3 L11: 2.0335 L22: 0.9026 REMARK 3 L33: 1.2839 L12: -0.4007 REMARK 3 L13: -0.0942 L23: 0.1505 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.0816 S13: 0.0782 REMARK 3 S21: -0.0223 S22: 0.1359 S23: 0.0676 REMARK 3 S31: 0.0295 S32: -0.0778 S33: -0.1363 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.6928 -8.8902 31.2356 REMARK 3 T TENSOR REMARK 3 T11: 0.8203 T22: 1.1732 REMARK 3 T33: 0.7381 T12: -0.1426 REMARK 3 T13: -0.1864 T23: 0.3022 REMARK 3 L TENSOR REMARK 3 L11: 2.6689 L22: 8.5617 REMARK 3 L33: 7.2476 L12: -2.2397 REMARK 3 L13: -4.2005 L23: 1.4709 REMARK 3 S TENSOR REMARK 3 S11: 0.3483 S12: 1.6623 S13: -0.5357 REMARK 3 S21: -1.0345 S22: 0.5335 S23: 0.5600 REMARK 3 S31: 0.2219 S32: 0.8906 S33: -0.7604 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 13 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.2001 -8.3725 30.5275 REMARK 3 T TENSOR REMARK 3 T11: 0.7862 T22: 1.5509 REMARK 3 T33: 0.8349 T12: -0.0207 REMARK 3 T13: -0.0905 T23: -0.1103 REMARK 3 L TENSOR REMARK 3 L11: 1.6295 L22: 8.0792 REMARK 3 L33: 7.2086 L12: -1.3503 REMARK 3 L13: -3.1577 L23: -0.1343 REMARK 3 S TENSOR REMARK 3 S11: -0.5987 S12: -0.0888 S13: -0.3670 REMARK 3 S21: -1.2364 S22: -0.0523 S23: 0.9129 REMARK 3 S31: -0.3108 S32: -0.0070 S33: 0.6503 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 7SFE 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_1000260100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-19 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 : 38168 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 42.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 6X9J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 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 80.98450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 80.98450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.24700 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 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 GLU A 736 CG CD OE1 OE2 REMARK 470 LYS A 739 CG CD CE NZ REMARK 470 LYS A 743 CG CD CE NZ REMARK 470 LYS A 748 CG CD CE NZ REMARK 470 LYS A 749 CD CE NZ REMARK 470 GLU A 758 CG CD OE1 OE2 REMARK 470 LYS A 772 CE NZ REMARK 470 LYS A 833 CG CD CE NZ REMARK 470 GLU A 841 CG CD OE1 OE2 REMARK 470 GLU A 852 CG CD OE1 OE2 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 GLU A 886 CG CD OE1 OE2 REMARK 470 ASP A 887 CG OD1 OD2 REMARK 470 ASN A 888 CG OD1 ND2 REMARK 470 LYS A 889 CG CD CE NZ REMARK 470 LYS A 891 CD CE NZ REMARK 470 GLU A 906 CD OE1 OE2 REMARK 470 GLU A 912 CG CD OE1 OE2 REMARK 470 GLU A 915 CG CD OE1 OE2 REMARK 470 ARG A 934 NE CZ NH1 NH2 REMARK 470 LYS A 951 CG CD CE NZ REMARK 470 LEU A 952 CG CD1 CD2 REMARK 470 VAL A 956 CG1 CG2 REMARK 470 LYS A 957 CG CD CE NZ REMARK 470 ARG A 958 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 960 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 961 CG CD CE NZ REMARK 470 GLU A 962 CG CD OE1 OE2 REMARK 470 ASP A 978 CG OD1 OD2 REMARK 470 LEU A 985 CG CD1 CD2 REMARK 470 LYS A 997 CE NZ REMARK 470 LYS A1054 CG CD CE NZ REMARK 470 GLU A1066 CG CD OE1 OE2 REMARK 470 LYS A1092 CG CD CE NZ REMARK 470 GLU A1097 CG CD OE1 OE2 REMARK 470 ARG A1104 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1135 CG CD CE NZ REMARK 470 LYS A1196 CD CE NZ REMARK 470 GLN A1227 CG CD OE1 NE2 REMARK 470 ARG A1234 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1238 CG CD NE CZ NH1 NH2 REMARK 470 SER A1241 OG REMARK 470 ARG A1276 CZ NH1 NH2 REMARK 470 ARG A1337 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1378 NE CZ NH1 NH2 REMARK 470 GLN A1404 CG CD OE1 NE2 REMARK 470 ARG A1462 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1463 CG CD CE NZ REMARK 470 GLU A1480 CG CD OE1 OE2 REMARK 470 LYS A1483 CG CD CE NZ REMARK 470 LYS A1535 CG CD CE NZ 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 LYS A 739 118.15 -161.99 REMARK 500 ASP A 753 -112.11 51.90 REMARK 500 THR A 862 -168.65 -77.63 REMARK 500 GLU A 912 119.10 -32.45 REMARK 500 LYS A 975 33.90 -99.95 REMARK 500 SER A1030 -161.15 -79.56 REMARK 500 MET A1371 23.49 -142.65 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 A2022 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2023 DISTANCE = 6.08 ANGSTROMS 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 A1703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 793 NE2 REMARK 620 2 CYS A 820 SG 107.9 REMARK 620 3 CYS A 893 SG 106.3 118.5 REMARK 620 4 CYS A 896 SG 101.0 102.5 118.9 REMARK 620 N 1 2 3 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 CYS A1476 SG REMARK 620 2 CYS A1478 SG 107.6 REMARK 620 3 CYS A1485 SG 129.4 103.6 REMARK 620 4 HIS A1502 NE2 114.3 92.2 103.1 REMARK 620 N 1 2 3 DBREF 7SFE A 729 1600 UNP P26358 DNMT1_HUMAN 393 1264 DBREF 7SFE C 1 12 PDB 7SFE 7SFE 1 12 DBREF 7SFE D 13 24 PDB 7SFE 7SFE 13 24 SEQADV 7SFE HIS A 727 UNP P26358 EXPRESSION TAG SEQADV 7SFE 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 EDO A1701 4 HET ZN A1702 1 HET ZN A1703 1 HET EDO A1704 4 HET EDO A1705 4 HET EDO A1706 4 HET EDO A1707 4 HET EDO A1708 4 HET EDO A1709 4 HET GOL A1710 6 HET 96I D 101 30 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM PYO 1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM 96I (2R)-2-{[6-(4-AMINOPIPERIDIN-1-YL)-3,5-DICYANO-4- HETNAM 2 96I ETHYLPYRIDIN-2-YL]AMINO}-2-PHENYLACETAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 3 PYO C9 H13 N2 O8 P FORMUL 4 EDO 7(C2 H6 O2) FORMUL 5 ZN 2(ZN 2+) FORMUL 13 GOL C3 H8 O3 FORMUL 14 96I C22 H25 N7 O FORMUL 15 HOH *225(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 ASP A 850 GLY A 857 1 8 HELIX 5 AA5 CYS A 893 ILE A 907 1 15 HELIX 6 AA6 GLU A 971 TYR A 976 5 6 HELIX 7 AA7 ARG A 1023 THR A 1027 5 5 HELIX 8 AA8 SER A 1030 TYR A 1035 5 6 HELIX 9 AA9 LYS A 1054 VAL A 1056 5 3 HELIX 10 AB1 GLU A 1066 LEU A 1068 5 3 HELIX 11 AB2 CYS A 1071 GLY A 1078 1 8 HELIX 12 AB3 PRO A 1100 ARG A 1104 5 5 HELIX 13 AB4 GLY A 1149 ALA A 1158 1 10 HELIX 14 AB5 TRP A 1170 ASN A 1181 1 12 HELIX 15 AB6 ASP A 1190 GLY A 1201 1 12 HELIX 16 AB7 ASN A 1236 ASN A 1245 1 10 HELIX 17 AB8 SER A 1246 ARG A 1259 1 14 HELIX 18 AB9 ASN A 1270 VAL A 1272 5 3 HELIX 19 AC1 SER A 1273 GLY A 1291 1 19 HELIX 20 AC2 GLY A 1302 GLY A 1305 5 4 HELIX 21 AC3 ALA A 1335 CYS A 1339 5 5 HELIX 22 AC4 THR A 1366 SER A 1372 1 7 HELIX 23 AC5 SER A 1394 GLY A 1402 1 9 HELIX 24 AC6 SER A 1418 HIS A 1427 1 10 HELIX 25 AC7 ASP A 1435 LEU A 1439 5 5 HELIX 26 AC8 CYS A 1476 GLU A 1480 5 5 HELIX 27 AC9 ASP A 1486 ARG A 1490 5 5 HELIX 28 AD1 TRP A 1498 THR A 1503 1 6 HELIX 29 AD2 GLY A 1504 ALA A 1511 5 8 HELIX 30 AD3 SER A 1549 GLN A 1557 1 9 HELIX 31 AD4 ASN A 1568 ALA A 1579 1 12 HELIX 32 AD5 PRO A 1581 ALA A 1598 1 18 SHEET 1 AA1 3 ILE A 731 TRP A 733 0 SHEET 2 AA1 3 LYS A 749 ILE A 752 -1 O CYS A 751 N SER A 732 SHEET 3 AA1 3 GLU A 755 GLU A 758 -1 O GLU A 755 N ILE A 752 SHEET 1 AA2 7 LYS A 739 ASP A 741 0 SHEET 2 AA2 7 LYS A 744 TYR A 746 -1 O TYR A 746 N LYS A 739 SHEET 3 AA2 7 TYR A 775 ASP A 785 -1 O GLU A 784 N SER A 745 SHEET 4 AA2 7 GLN A 790 ALA A 799 -1 O PHE A 797 N LEU A 776 SHEET 5 AA2 7 GLU A 813 GLN A 824 -1 O GLU A 821 N ALA A 794 SHEET 6 AA2 7 TYR A 863 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 7 AA2 7 VAL A 834 TYR A 836 1 N ILE A 835 O TYR A 863 SHEET 1 AA3 7 ILE A 828 VAL A 832 0 SHEET 2 AA3 7 CYS A 762 VAL A 765 -1 N SER A 764 O HIS A 829 SHEET 3 AA3 7 TYR A 775 ASP A 785 -1 O ALA A 777 N VAL A 763 SHEET 4 AA3 7 GLN A 790 ALA A 799 -1 O PHE A 797 N LEU A 776 SHEET 5 AA3 7 GLU A 813 GLN A 824 -1 O GLU A 821 N ALA A 794 SHEET 6 AA3 7 TYR A 863 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 7 AA3 7 ARG A 875 GLU A 877 -1 O GLU A 877 N TRP A 868 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 9 GLN A 913 ASP A 916 0 SHEET 2 AA5 9 ARG A 920 TYR A 923 -1 O LEU A 922 N GLU A 915 SHEET 3 AA5 9 ARG A 992 PRO A1002 -1 O ILE A 999 N TYR A 923 SHEET 4 AA5 9 LYS A1015 TYR A1022 -1 O LYS A1015 N PHE A1000 SHEET 5 AA5 9 LEU A1041 ASP A1052 -1 O ALA A1049 N VAL A1018 SHEET 6 AA5 9 ARG A1082 ALA A1088 1 O TYR A1084 N LEU A1042 SHEET 7 AA5 9 GLY A1058 TYR A1064 1 N GLU A1063 O PHE A1083 SHEET 8 AA5 9 GLY A 938 LEU A 941 -1 N TYR A 940 O GLY A1058 SHEET 9 AA5 9 ARG A 992 PRO A1002 -1 O GLY A 994 N VAL A 939 SHEET 1 AA6 7 THR A1185 PHE A1187 0 SHEET 2 AA6 7 SER A1161 ILE A1167 1 N ALA A1166 O PHE A1187 SHEET 3 AA6 7 LEU A1139 VAL A1144 1 N THR A1141 O ASP A1162 SHEET 4 AA6 7 MET A1219 GLY A1222 1 O MET A1219 N LEU A1142 SHEET 5 AA6 7 PHE A1262 VAL A1268 1 O PHE A1262 N LEU A1220 SHEET 6 AA6 7 ARG A1311 ALA A1318 -1 O ILE A1315 N LEU A1265 SHEET 7 AA6 7 GLN A1293 GLN A1300 -1 N GLY A1297 O ILE A1314 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 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 1.61 LINK NE2 HIS A 793 ZN ZN A1703 1555 1555 2.03 LINK SG CYS A 820 ZN ZN A1703 1555 1555 2.31 LINK SG CYS A 893 ZN ZN A1703 1555 1555 2.33 LINK SG CYS A 896 ZN ZN A1703 1555 1555 2.28 LINK SG CYS A1476 ZN ZN A1702 1555 1555 2.28 LINK SG CYS A1478 ZN ZN A1702 1555 1555 2.28 LINK SG CYS A1485 ZN ZN A1702 1555 1555 2.27 LINK NE2 HIS A1502 ZN ZN A1702 1555 1555 2.04 CRYST1 161.969 78.494 117.562 90.00 125.83 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 0.006174 0.000000 0.004458 0.00000 SCALE2 0.000000 0.012740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010492 0.00000