data_3NGD # _model_server_result.job_id bxK1FZlPzFrXv8DpwOCs6Q _model_server_result.datetime_utc '2024-10-12 10:20:51' _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 3ngd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":875}' # _entry.id 3NGD # _exptl.entry_id 3NGD _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 3NGD _cell.length_a 97.999 _cell.length_b 97.999 _cell.length_c 202.552 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NGD _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 PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _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 A O3' DC 17 C DC 12 1_555 A P DOC 18 C DOC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? covale ? covale2 B O3' 6OG 4 D 6OG 840 1_555 B P DG 5 D DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.576 ? hydrog WATSON-CRICK hydrog1 A N1 DA 12 C DA 7 1_555 B N3 DT 11 D DT 847 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 DA 12 C DA 7 1_555 B O4 DT 11 D DT 847 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 13 C DG 8 1_555 B N3 DC 10 D DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 13 C DG 8 1_555 B O2 DC 10 D DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 13 C DG 8 1_555 B N4 DC 10 D DC 846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DG 14 C DG 9 1_555 B N3 DC 9 D DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 14 C DG 9 1_555 B O2 DC 9 D DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 14 C DG 9 1_555 B N4 DC 9 D DC 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 15 C DA 10 1_555 B N3 DT 8 D DT 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 15 C DA 10 1_555 B O4 DT 8 D DT 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 16 C DC 11 1_555 B N1 DG 7 D DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 16 C DC 11 1_555 B O6 DG 7 D DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 16 C DC 11 1_555 B N2 DG 7 D DG 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 DC 17 C DC 12 1_555 B N1 DG 6 D DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N4 DC 17 C DC 12 1_555 B O6 DG 6 D DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O2 DC 17 C DC 12 1_555 B N2 DG 6 D DG 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DOC 18 C DOC 13 1_555 B N1 DG 5 D DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DOC 18 C DOC 13 1_555 B O6 DG 5 D DG 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 DOC 18 C DOC 13 1_555 B N2 DG 5 D 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 198 n n N1 C6 DCP sing 199 n n N1 C1' DCP sing 200 n n C2 N3 DCP sing 201 n n C2 O2 DCP doub 202 n n N3 C4 DCP doub 203 n n C4 C5 DCP sing 204 n n C4 N4 DCP sing 205 n n C5 C6 DCP doub 206 n n C5 H5 DCP sing 207 n n C6 H6 DCP sing 208 n n N4 HN41 DCP sing 209 n n N4 HN42 DCP sing 210 n n C1' C2' DCP sing 211 n n C1' O4' DCP sing 212 n n C1' H1' DCP sing 213 n n C2' C3' DCP sing 214 n n C2' "H2'1" DCP sing 215 n n C2' "H2'2" DCP sing 216 n n C3' C4' DCP sing 217 n n C3' O3' DCP sing 218 n n C3' H3' DCP sing 219 n n C4' O4' DCP sing 220 n n C4' C5' DCP sing 221 n n C4' H4' DCP sing 222 n n O3' HO3' DCP sing 223 n n C5' O5' DCP sing 224 n n C5' "H5'1" DCP sing 225 n n C5' "H5'2" DCP sing 226 n n O5' PA DCP sing 227 n n PA O1A DCP doub 228 n n PA O2A DCP sing 229 n n PA O3A DCP sing 230 n n O2A HOA2 DCP sing 231 n n O3A PB DCP sing 232 n n PB O1B DCP doub 233 n n PB O2B DCP sing 234 n n PB O3B DCP sing 235 n n O2B HOB2 DCP sing 236 n n O3B PG DCP sing 237 n n PG O1G DCP doub 238 n n PG O2G DCP sing 239 n n PG O3G DCP sing 240 n n O2G HOG2 DCP sing 241 n n O3G HOG3 DCP sing 242 n n # _atom_sites.entry_id 3NGD _atom_sites.fract_transf_matrix[1][1] 0.010204 _atom_sites.fract_transf_matrix[1][2] 0.005891 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011783 _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] 0.004937 _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 HOH C 1 14 12 HOH HOH . E 4 HOH C 2 27 27 HOH HOH . E 4 HOH C 3 35 35 HOH HOH . E 4 HOH C 4 46 46 HOH HOH . F 4 HOH D 1 8 8 HOH HOH . F 4 HOH D 2 13 13 HOH HOH . F 4 HOH D 3 20 20 HOH HOH . F 4 HOH D 4 23 23 HOH HOH . F 4 HOH D 5 28 28 HOH HOH . F 4 HOH D 6 69 69 HOH HOH . F 4 HOH D 7 72 72 HOH HOH . F 4 HOH D 8 79 79 HOH HOH . G 4 HOH A 1 421 1 HOH HOH . G 4 HOH A 2 422 5 HOH HOH . G 4 HOH A 3 423 6 HOH HOH . G 4 HOH A 4 424 7 HOH HOH . G 4 HOH A 5 425 10 HOH HOH . G 4 HOH A 6 426 11 HOH HOH . G 4 HOH A 7 427 14 HOH HOH . G 4 HOH A 8 428 15 HOH HOH . G 4 HOH A 9 429 16 HOH HOH . G 4 HOH A 10 430 18 HOH HOH . G 4 HOH A 11 431 19 HOH HOH . G 4 HOH A 12 432 24 HOH HOH . G 4 HOH A 13 433 25 HOH HOH . G 4 HOH A 14 434 29 HOH HOH . G 4 HOH A 15 435 30 HOH HOH . G 4 HOH A 16 436 32 HOH HOH . G 4 HOH A 17 437 33 HOH HOH . G 4 HOH A 18 438 34 HOH HOH . G 4 HOH A 19 439 36 HOH HOH . G 4 HOH A 20 440 37 HOH HOH . G 4 HOH A 21 441 38 HOH HOH . G 4 HOH A 22 442 39 HOH HOH . G 4 HOH A 23 443 40 HOH HOH . G 4 HOH A 24 444 41 HOH HOH . G 4 HOH A 25 445 42 HOH HOH . G 4 HOH A 26 446 43 HOH HOH . G 4 HOH A 27 447 45 HOH HOH . G 4 HOH A 28 448 47 HOH HOH . G 4 HOH A 29 449 48 HOH HOH . G 4 HOH A 30 450 49 HOH HOH . G 4 HOH A 31 451 52 HOH HOH . G 4 HOH A 32 452 53 HOH HOH . G 4 HOH A 33 453 54 HOH HOH . G 4 HOH A 34 454 56 HOH HOH . G 4 HOH A 35 455 58 HOH HOH . G 4 HOH A 36 456 59 HOH HOH . G 4 HOH A 37 457 60 HOH HOH . G 4 HOH A 38 458 62 HOH HOH . G 4 HOH A 39 459 63 HOH HOH . G 4 HOH A 40 460 64 HOH HOH . G 4 HOH A 41 461 65 HOH HOH . G 4 HOH A 42 462 66 HOH HOH . G 4 HOH A 43 463 67 HOH HOH . G 4 HOH A 44 464 68 HOH HOH . G 4 HOH A 45 465 70 HOH HOH . G 4 HOH A 46 466 71 HOH HOH . G 4 HOH A 47 467 73 HOH HOH . G 4 HOH A 48 468 74 HOH HOH . G 4 HOH A 49 469 75 HOH HOH . G 4 HOH A 50 470 77 HOH HOH . G 4 HOH A 51 471 78 HOH HOH . G 4 HOH A 52 472 80 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 -1.192 -25.419 19.271 1 49.45 ? N1 DCP 875 A 1 HETATM 2 C C2 DCP . . . D 3 -0.243 -26.357 19.73 1 50.79 ? C2 DCP 875 A 1 HETATM 3 N N3 DCP . . . D 3 0.446 -27.202 18.781 1 49.57 ? N3 DCP 875 A 1 HETATM 4 C C4 DCP . . . D 3 0.171 -27.087 17.366 1 49.03 ? C4 DCP 875 A 1 HETATM 5 C C5 DCP . . . D 3 -0.762 -26.155 16.952 1 48.92 ? C5 DCP 875 A 1 HETATM 6 C C6 DCP . . . D 3 -1.42 -25.347 17.885 1 50.04 ? C6 DCP 875 A 1 HETATM 7 O O2 DCP . . . D 3 -0.039 -26.433 20.947 1 50.65 ? O2 DCP 875 A 1 HETATM 8 N N4 DCP . . . D 3 0.775 -27.824 16.407 1 48.06 ? N4 DCP 875 A 1 HETATM 9 C C1' DCP . . . D 3 -1.915 -24.524 20.225 1 49.29 ? C1' DCP 875 A 1 HETATM 10 C C2' DCP . . . D 3 -1.189 -23.154 20.302 1 50.04 ? C2' DCP 875 A 1 HETATM 11 C C3' DCP . . . D 3 -2.155 -22.117 19.694 1 51.59 ? C3' DCP 875 A 1 HETATM 12 C C4' DCP . . . D 3 -3.449 -22.894 19.324 1 52.67 ? C4' DCP 875 A 1 HETATM 13 O O4' DCP . . . D 3 -3.318 -24.264 19.858 1 50.67 ? O4' DCP 875 A 1 HETATM 14 O O3' DCP . . . D 3 -2.468 -21.024 20.603 1 48.63 ? O3' DCP 875 A 1 HETATM 15 C C5' DCP . . . D 3 -3.744 -22.889 17.776 1 54.05 ? C5' DCP 875 A 1 HETATM 16 O O5' DCP . . . D 3 -2.551 -22.869 16.885 1 55.9 ? O5' DCP 875 A 1 HETATM 17 P PA DCP . . . D 3 -2.525 -22.244 15.264 1 59.22 ? PA DCP 875 A 1 HETATM 18 O O1A DCP . . . D 3 -3.932 -22.064 14.722 1 56.75 ? O1A DCP 875 A 1 HETATM 19 O O2A DCP . . . D 3 -1.552 -23.103 14.502 1 58.49 ? O2A DCP 875 A 1 HETATM 20 O O3A DCP . . . D 3 -1.786 -20.735 15.507 1 56.31 ? O3A DCP 875 A 1 HETATM 21 P PB DCP . . . D 3 -2.4 -19.43 16.424 1 56.69 ? PB DCP 875 A 1 HETATM 22 O O1B DCP . . . D 3 -1.978 -19.694 17.86 1 51.44 ? O1B DCP 875 A 1 HETATM 23 O O2B DCP . . . D 3 -3.883 -19.232 16.117 1 51.59 ? O2B DCP 875 A 1 HETATM 24 O O3B DCP . . . D 3 -1.43 -18.124 15.648 1 49.77 ? O3B DCP 875 A 1 HETATM 25 P PG DCP . . . D 3 -1.612 -17.694 14.035 1 45.17 ? PG DCP 875 A 1 HETATM 26 O O1G DCP . . . D 3 -2.957 -18.063 13.491 1 44.34 ? O1G DCP 875 A 1 HETATM 27 O O2G DCP . . . D 3 -0.408 -18.447 13.246 1 44.56 ? O2G DCP 875 A 1 HETATM 28 O O3G DCP . . . D 3 -1.364 -16.141 13.787 1 42.45 ? O3G DCP 875 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #