data_3EPG # _model_server_result.job_id d159leoNs9VWkOVsuohaBA _model_server_result.datetime_utc '2024-11-16 01:45:57' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3epg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":875}' # _entry.id 3EPG # _exptl.entry_id 3EPG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3EPG _cell.length_a 98.535 _cell.length_b 98.535 _cell.length_c 202.354 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EPG _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -49.2675 -85.333813 33.725667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B O3' DC 17 B DC 12 1_555 B P DOC 18 B DOC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.502 ? covale ? covale2 C O3' 2EG 4 C 2EG 840 1_555 C P DG 5 C DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? metalc ? metalc1 A O LYS 237 A LYS 237 1_555 E NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc2 A O ILE 239 A ILE 239 1_555 E NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc3 A O ILE 242 A ILE 242 1_555 E NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc4 E NA NA . A NA 421 1_555 B OP1 DC 17 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? hydrog WATSON-CRICK hydrog1 B N1 DA 12 B DA 7 1_555 C N3 DT 11 C DT 847 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 12 B DA 7 1_555 C O4 DT 11 C DT 847 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 13 B DG 8 1_555 C N3 DC 10 C DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 13 B DG 8 1_555 C O2 DC 10 C DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 13 B DG 8 1_555 C N4 DC 10 C DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 14 B DG 9 1_555 C N3 DC 9 C DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 14 B DG 9 1_555 C O2 DC 9 C DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 14 B DG 9 1_555 C N4 DC 9 C DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 15 B DA 10 1_555 C N3 DT 8 C DT 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 15 B DA 10 1_555 C O4 DT 8 C DT 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 16 B DC 11 1_555 C N1 DG 7 C DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 16 B DC 11 1_555 C O6 DG 7 C DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 16 B DC 11 1_555 C N2 DG 7 C DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 17 B DC 12 1_555 C N1 DG 6 C DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 17 B DC 12 1_555 C O6 DG 6 C DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 17 B DC 12 1_555 C N2 DG 6 C DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DOC 18 B DOC 13 1_555 C N1 DG 5 C DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N4 DOC 18 B DOC 13 1_555 C O6 DG 5 C DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O2 DOC 18 B DOC 13 1_555 C N2 DG 5 C DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DCP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 DCP sing 201 n n N1 C6 DCP sing 202 n n N1 C1' DCP sing 203 n n C2 N3 DCP sing 204 n n C2 O2 DCP doub 205 n n N3 C4 DCP doub 206 n n C4 C5 DCP sing 207 n n C4 N4 DCP sing 208 n n C5 C6 DCP doub 209 n n C5 H5 DCP sing 210 n n C6 H6 DCP sing 211 n n N4 HN41 DCP sing 212 n n N4 HN42 DCP sing 213 n n C1' C2' DCP sing 214 n n C1' O4' DCP sing 215 n n C1' H1' DCP sing 216 n n C2' C3' DCP sing 217 n n C2' "H2'1" DCP sing 218 n n C2' "H2'2" DCP sing 219 n n C3' C4' DCP sing 220 n n C3' O3' DCP sing 221 n n C3' H3' DCP sing 222 n n C4' O4' DCP sing 223 n n C4' C5' DCP sing 224 n n C4' H4' DCP sing 225 n n O3' HO3' DCP sing 226 n n C5' O5' DCP sing 227 n n C5' "H5'1" DCP sing 228 n n C5' "H5'2" DCP sing 229 n n O5' PA DCP sing 230 n n PA O1A DCP doub 231 n n PA O2A DCP sing 232 n n PA O3A DCP sing 233 n n O2A HOA2 DCP sing 234 n n O3A PB DCP sing 235 n n PB O1B DCP doub 236 n n PB O2B DCP sing 237 n n PB O3B DCP sing 238 n n O2B HOB2 DCP sing 239 n n O3B PG DCP sing 240 n n PG O1G DCP doub 241 n n PG O2G DCP sing 242 n n PG O3G DCP sing 243 n n O2G HOG2 DCP sing 244 n n O3G HOG3 DCP sing 245 n n # _atom_sites.entry_id 3EPG _atom_sites.fract_transf_matrix[1][1] 0.010149 _atom_sites.fract_transf_matrix[1][2] 0.005859 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011719 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004942 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 3 DCP A 1 875 875 DCP DCP . E 4 NA A 1 421 1 NA NA . F 4 NA A 1 422 2 NA NA . G 4 NA A 1 423 1 NA NA . H 4 NA C 1 1 1 NA NA . I 5 HOH A 1 424 1 HOH HOH . I 5 HOH A 2 425 3 HOH HOH . I 5 HOH A 3 426 4 HOH HOH . I 5 HOH A 4 427 5 HOH HOH . I 5 HOH A 5 428 7 HOH HOH . I 5 HOH A 6 429 8 HOH HOH . I 5 HOH A 7 430 9 HOH HOH . I 5 HOH A 8 431 10 HOH HOH . I 5 HOH A 9 432 11 HOH HOH . I 5 HOH A 10 433 13 HOH HOH . I 5 HOH A 11 434 14 HOH HOH . I 5 HOH A 12 435 15 HOH HOH . I 5 HOH A 13 436 17 HOH HOH . I 5 HOH A 14 437 18 HOH HOH . I 5 HOH A 15 438 20 HOH HOH . I 5 HOH A 16 439 21 HOH HOH . I 5 HOH A 17 440 24 HOH HOH . I 5 HOH A 18 441 26 HOH HOH . I 5 HOH A 19 442 27 HOH HOH . I 5 HOH A 20 443 28 HOH HOH . I 5 HOH A 21 444 29 HOH HOH . I 5 HOH A 22 445 31 HOH HOH . I 5 HOH A 23 446 32 HOH HOH . I 5 HOH A 24 447 34 HOH HOH . I 5 HOH A 25 448 35 HOH HOH . I 5 HOH A 26 449 36 HOH HOH . I 5 HOH A 27 450 37 HOH HOH . I 5 HOH A 28 451 39 HOH HOH . I 5 HOH A 29 452 40 HOH HOH . I 5 HOH A 30 453 41 HOH HOH . I 5 HOH A 31 454 42 HOH HOH . I 5 HOH A 32 455 43 HOH HOH . I 5 HOH A 33 456 44 HOH HOH . I 5 HOH A 34 457 45 HOH HOH . I 5 HOH A 35 458 46 HOH HOH . I 5 HOH A 36 459 47 HOH HOH . I 5 HOH A 37 460 48 HOH HOH . I 5 HOH A 38 461 50 HOH HOH . I 5 HOH A 39 462 51 HOH HOH . I 5 HOH A 40 463 52 HOH HOH . I 5 HOH A 41 464 53 HOH HOH . I 5 HOH A 42 465 54 HOH HOH . I 5 HOH A 43 466 55 HOH HOH . I 5 HOH A 44 467 56 HOH HOH . I 5 HOH A 45 468 57 HOH HOH . I 5 HOH A 46 469 58 HOH HOH . I 5 HOH A 47 470 59 HOH HOH . I 5 HOH A 48 471 60 HOH HOH . I 5 HOH A 49 472 61 HOH HOH . I 5 HOH A 50 473 62 HOH HOH . I 5 HOH A 51 474 63 HOH HOH . I 5 HOH A 52 475 64 HOH HOH . I 5 HOH A 53 476 65 HOH HOH . I 5 HOH A 54 477 66 HOH HOH . I 5 HOH A 55 478 67 HOH HOH . I 5 HOH A 56 479 68 HOH HOH . I 5 HOH A 57 480 69 HOH HOH . I 5 HOH A 58 481 70 HOH HOH . I 5 HOH A 59 482 71 HOH HOH . I 5 HOH A 60 483 72 HOH HOH . I 5 HOH A 61 484 73 HOH HOH . I 5 HOH A 62 485 74 HOH HOH . I 5 HOH A 63 486 75 HOH HOH . I 5 HOH A 64 487 76 HOH HOH . I 5 HOH A 65 488 77 HOH HOH . I 5 HOH A 66 489 78 HOH HOH . I 5 HOH A 67 490 79 HOH HOH . J 5 HOH C 1 23 23 HOH HOH . J 5 HOH C 2 49 49 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 DCP . . . D 3 -1.892 -25.168 19.432 1 47.02 ? N1 DCP 875 A 1 HETATM 2 C C2 DCP . . . D 3 -1.193 -26.021 20.222 1 47.19 ? C2 DCP 875 A 1 HETATM 3 N N3 DCP . . . D 3 -0.455 -27.053 19.741 1 47.56 ? N3 DCP 875 A 1 HETATM 4 C C4 DCP . . . D 3 -0.41 -27.248 18.407 1 47.73 ? C4 DCP 875 A 1 HETATM 5 C C5 DCP . . . D 3 -1.102 -26.407 17.572 1 47.79 ? C5 DCP 875 A 1 HETATM 6 C C6 DCP . . . D 3 -1.838 -25.358 18.081 1 47.35 ? C6 DCP 875 A 1 HETATM 7 O O2 DCP . . . D 3 -1.222 -25.88 21.409 1 47.18 ? O2 DCP 875 A 1 HETATM 8 N N4 DCP . . . D 3 0.302 -28.229 17.934 1 47.51 ? N4 DCP 875 A 1 HETATM 9 C C1' DCP . . . D 3 -2.647 -24.071 20.046 1 48.57 ? C1' DCP 875 A 1 HETATM 10 C C2' DCP . . . D 3 -1.857 -22.785 20.134 1 51.01 ? C2' DCP 875 A 1 HETATM 11 C C3' DCP . . . D 3 -2.655 -21.738 19.397 1 50.94 ? C3' DCP 875 A 1 HETATM 12 C C4' DCP . . . D 3 -3.979 -22.428 19.075 1 51.34 ? C4' DCP 875 A 1 HETATM 13 O O4' DCP . . . D 3 -3.938 -23.733 19.647 1 50.32 ? O4' DCP 875 A 1 HETATM 14 O O3' DCP . . . D 3 -2.84 -20.626 20.235 1 50 ? O3' DCP 875 A 1 HETATM 15 C C5' DCP . . . D 3 -4.879 -22.375 17.761 1 51.85 ? C5' DCP 875 A 1 HETATM 16 O O5' DCP . . . D 3 -4.261 -22.787 16.507 1 52.77 ? O5' DCP 875 A 1 HETATM 17 P PA DCP . . . D 3 -3.545 -22.047 15.341 1 54.3 ? PA DCP 875 A 1 HETATM 18 O O1A DCP . . . D 3 -4.479 -21.241 14.585 1 51.62 ? O1A DCP 875 A 1 HETATM 19 O O2A DCP . . . D 3 -2.823 -23.051 14.635 1 52.93 ? O2A DCP 875 A 1 HETATM 20 O O3A DCP . . . D 3 -2.443 -21.285 16.027 1 51.36 ? O3A DCP 875 A 1 HETATM 21 P PB DCP . . . D 3 -2.583 -19.816 16.49 1 49.82 ? PB DCP 875 A 1 HETATM 22 O O1B DCP . . . D 3 -1.791 -19.782 17.68 1 49.25 ? O1B DCP 875 A 1 HETATM 23 O O2B DCP . . . D 3 -3.984 -19.444 16.593 1 45.72 ? O2B DCP 875 A 1 HETATM 24 O O3B DCP . . . D 3 -1.819 -18.87 15.444 1 46.85 ? O3B DCP 875 A 1 HETATM 25 P PG DCP . . . D 3 -2.047 -18.104 14.085 1 44.35 ? PG DCP 875 A 1 HETATM 26 O O1G DCP . . . D 3 -3.307 -17.69 13.662 1 43.72 ? O1G DCP 875 A 1 HETATM 27 O O2G DCP . . . D 3 -1.352 -18.764 13.044 1 43.47 ? O2G DCP 875 A 1 HETATM 28 O O3G DCP . . . D 3 -1.295 -16.952 14.334 1 43.68 ? O3G DCP 875 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #