data_2J4H # _model_server_result.job_id EgHs4jQQoLPcYW1CA03vJQ _model_server_result.datetime_utc '2024-11-16 02:34:18' _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 2j4h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1175}' # _entry.id 2J4H # _exptl.entry_id 2J4H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 387.177 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DEOXYCYTIDINE DIPHOSPHATE' _entity.pdbx_number_of_molecules 2 _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 2J4H _cell.length_a 62.545 _cell.length_b 62.545 _cell.length_c 342.444 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J4H _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS trimeric 3 software_defined_assembly 1 PQS trimeric 3 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E 1 1,2,3 B,F,G,H 2 1,4,5 # 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' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 62.545 0 0 5 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 31.2725 -54.165559 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 metalc ? metalc1 A O ALA 121 A ALA 121 1_555 E MG MG . A MG 1177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc2 A N VAL 122 A VAL 122 1_555 E MG MG . A MG 1177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc3 C O1A YYY . A YYY 1175 1_555 D MG MG . A MG 1176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 C O1B YYY . A YYY 1175 1_555 D MG MG . A MG 1176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc5 B O ALA 121 B ALA 121 1_555 H MG MG . B MG 1175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc6 B N VAL 122 B VAL 122 1_555 H MG MG . B MG 1175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc7 F O1A YYY . B YYY 1173 1_555 G MG MG . B MG 1174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc8 F O1B YYY . B YYY 1173 1_555 G MG MG . B MG 1174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? # _chem_comp.formula 'C9 H15 N3 O10 P2' _chem_comp.formula_weight 387.177 _chem_comp.id YYY _chem_comp.mon_nstd_flag . _chem_comp.name 'DEOXYCYTIDINE DIPHOSPHATE' _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 O3B H3B YYY sing 374 n n O3B PB YYY sing 375 n n PB O1B YYY doub 376 n n PB O2B YYY sing 377 n n PB O3A YYY sing 378 n n O2B H2B YYY sing 379 n n O3A PA YYY sing 380 n n PA O1A YYY doub 381 n n PA O2A YYY sing 382 n n PA O5' YYY sing 383 n n O2A H2A YYY sing 384 n n O5' C5' YYY sing 385 n n C5' C4' YYY sing 386 n n C5' "H5'1" YYY sing 387 n n C5' "H5'2" YYY sing 388 n n C4' O4' YYY sing 389 n n C4' C3' YYY sing 390 n n C4' H4' YYY sing 391 n n O4' C1' YYY sing 392 n n C3' O3' YYY sing 393 n n C3' C2' YYY sing 394 n n C3' H3' YYY sing 395 n n O3' HA YYY sing 396 n n C2' C1' YYY sing 397 n n C2' "H2'1" YYY sing 398 n n C2' "H2'2" YYY sing 399 n n C1' N1 YYY sing 400 n n C1' H1' YYY sing 401 n n N1 C2 YYY sing 402 n n N1 C6 YYY sing 403 n n C2 O2 YYY doub 404 n n C2 N3 YYY sing 405 n n N3 C4 YYY doub 406 n n C4 N4 YYY sing 407 n n C4 C5 YYY sing 408 n n N4 H4N1 YYY sing 409 n n N4 H4N2 YYY sing 410 n n C5 C6 YYY doub 411 n n C5 H5 YYY sing 412 n n C6 H6 YYY sing 413 n n # _atom_sites.entry_id 2J4H _atom_sites.fract_transf_matrix[1][1] 0.015988 _atom_sites.fract_transf_matrix[1][2] 0.009231 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018462 _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] 0.00292 _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 C 2 YYY A 1 1175 1175 YYY YYY . D 3 MG A 1 1176 1176 MG MG . E 3 MG A 1 1177 1177 MG MG . F 2 YYY B 1 1173 1173 YYY YYY . G 3 MG B 1 1174 1174 MG MG . H 3 MG B 1 1175 1175 MG MG . # 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 O O3B YYY . . . C 2 11.481 -10.07 20.745 1 40.54 ? O3B YYY 1175 A 1 HETATM 2 P PB YYY . . . C 2 11.937 -9.818 22.248 1 38.36 ? PB YYY 1175 A 1 HETATM 3 O O1B YYY . . . C 2 11.23 -10.919 23.134 1 38.08 ? O1B YYY 1175 A 1 HETATM 4 O O2B YYY . . . C 2 13.541 -9.886 22.367 1 38.89 ? O2B YYY 1175 A 1 HETATM 5 O O3A YYY . . . C 2 11.583 -8.275 22.662 1 38.59 ? O3A YYY 1175 A 1 HETATM 6 P PA YYY . . . C 2 10.61 -7.76 23.86 1 38.13 ? PA YYY 1175 A 1 HETATM 7 O O1A YYY . . . C 2 10.401 -8.937 24.9 1 38.51 ? O1A YYY 1175 A 1 HETATM 8 O O2A YYY . . . C 2 9.197 -7.212 23.342 1 37.95 ? O2A YYY 1175 A 1 HETATM 9 O O5' YYY . . . C 2 11.471 -6.586 24.51 1 37.03 ? O5' YYY 1175 A 1 HETATM 10 C C5' YYY . . . C 2 12.633 -6.974 25.199 1 37.09 ? C5' YYY 1175 A 1 HETATM 11 C C4' YYY . . . C 2 13.523 -5.772 25.463 1 37.69 ? C4' YYY 1175 A 1 HETATM 12 O O4' YYY . . . C 2 13.892 -5.032 24.291 1 36.9 ? O4' YYY 1175 A 1 HETATM 13 C C3' YYY . . . C 2 12.97 -4.801 26.511 1 36.82 ? C3' YYY 1175 A 1 HETATM 14 O O3' YYY . . . C 2 13.557 -4.958 27.785 1 35.43 ? O3' YYY 1175 A 1 HETATM 15 C C2' YYY . . . C 2 13.218 -3.427 25.942 1 37.26 ? C2' YYY 1175 A 1 HETATM 16 C C1' YYY . . . C 2 13.775 -3.628 24.532 1 36.93 ? C1' YYY 1175 A 1 HETATM 17 N N1 YYY . . . C 2 12.886 -2.894 23.608 1 37.07 ? N1 YYY 1175 A 1 HETATM 18 C C2 YYY . . . C 2 13.417 -2.005 22.642 1 36.63 ? C2 YYY 1175 A 1 HETATM 19 O O2 YYY . . . C 2 14.663 -1.861 22.53 1 36.3 ? O2 YYY 1175 A 1 HETATM 20 N N3 YYY . . . C 2 12.558 -1.321 21.833 1 36.76 ? N3 YYY 1175 A 1 HETATM 21 C C4 YYY . . . C 2 11.209 -1.456 21.929 1 36.74 ? C4 YYY 1175 A 1 HETATM 22 N N4 YYY . . . C 2 10.373 -0.77 21.115 1 36.61 ? N4 YYY 1175 A 1 HETATM 23 C C5 YYY . . . C 2 10.683 -2.319 22.878 1 36.95 ? C5 YYY 1175 A 1 HETATM 24 C C6 YYY . . . C 2 11.544 -3.021 23.712 1 37.2 ? C6 YYY 1175 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #