data_3DCO # _model_server_result.job_id '_H_6oqjXEV6fMBHjm0eonA' _model_server_result.datetime_utc '2025-03-13 15:29:53' _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 3dco # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 3DCO # _exptl.entry_id 3DCO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 3DCO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DCO _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _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 5 _struct_asym.id E _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 metalc ? metalc1 A OG SER 109 N SER 94 1_555 D MG MG . N MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc2 E O2B ADP . N ADP 401 1_555 D MG MG . N MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 F MG MG . A MG 501 1_555 H O1G GTP . B GTP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3DCO _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 4 MG N 1 402 402 MG MG . E 5 ADP N 1 401 401 ADP ADP . F 4 MG A 1 501 501 MG MG . G 6 ZN A 1 900 900 ZN ZN . H 7 GTP B 1 500 500 GTP GTP . I 8 GDP B 1 600 600 GDP GDP . J 9 TA1 B 1 601 601 TA1 TA1 . # 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 P PB ADP . . . E 5 139.574 25.139 54.896 1 21.61 ? PB ADP 401 N 1 HETATM 2 O O1B ADP . . . E 5 139.264 23.843 55.528 1 20.88 ? O1B ADP 401 N 1 HETATM 3 O O2B ADP . . . E 5 140.087 24.879 53.438 1 21.88 ? O2B ADP 401 N 1 HETATM 4 O O3B ADP . . . E 5 138.144 26.021 54.912 1 19.39 ? O3B ADP 401 N 1 HETATM 5 P PA ADP . . . E 5 142.04 26.364 54.999 1 26.15 ? PA ADP 401 N 1 HETATM 6 O O1A ADP . . . E 5 142.677 25.186 54.443 1 25.77 ? O1A ADP 401 N 1 HETATM 7 O O2A ADP . . . E 5 141.641 27.391 53.861 1 28.02 ? O2A ADP 401 N 1 HETATM 8 O O3A ADP . . . E 5 140.692 25.886 55.817 1 24.15 ? O3A ADP 401 N 1 HETATM 9 O O5' ADP . . . E 5 143.013 27.027 56.083 1 29.16 ? O5' ADP 401 N 1 HETATM 10 C C5' ADP . . . E 5 142.41 28.214 56.615 1 28.72 ? C5' ADP 401 N 1 HETATM 11 C C4' ADP . . . E 5 143.523 29.138 57.117 1 28.12 ? C4' ADP 401 N 1 HETATM 12 O O4' ADP . . . E 5 144.282 28.501 58.175 1 26.35 ? O4' ADP 401 N 1 HETATM 13 C C3' ADP . . . E 5 144.543 29.463 55.961 1 28.74 ? C3' ADP 401 N 1 HETATM 14 O O3' ADP . . . E 5 145.305 30.627 56.253 1 34.17 ? O3' ADP 401 N 1 HETATM 15 C C2' ADP . . . E 5 145.588 28.308 56.253 1 27.58 ? C2' ADP 401 N 1 HETATM 16 O O2' ADP . . . E 5 146.89 28.664 55.761 1 28.13 ? O2' ADP 401 N 1 HETATM 17 C C1' ADP . . . E 5 145.651 28.28 57.804 1 27.17 ? C1' ADP 401 N 1 HETATM 18 N N9 ADP . . . E 5 146.069 26.962 58.279 1 26.24 ? N9 ADP 401 N 1 HETATM 19 C C8 ADP . . . E 5 145.277 25.841 58.369 1 22.73 ? C8 ADP 401 N 1 HETATM 20 N N7 ADP . . . E 5 145.996 24.793 58.703 1 24.03 ? N7 ADP 401 N 1 HETATM 21 C C5 ADP . . . E 5 147.24 25.22 59.045 1 24.49 ? C5 ADP 401 N 1 HETATM 22 C C6 ADP . . . E 5 148.439 24.592 59.467 1 23.87 ? C6 ADP 401 N 1 HETATM 23 N N6 ADP . . . E 5 148.443 23.253 59.812 1 24.96 ? N6 ADP 401 N 1 HETATM 24 N N1 ADP . . . E 5 149.57 25.332 59.558 1 24.86 ? N1 ADP 401 N 1 HETATM 25 C C2 ADP . . . E 5 149.553 26.654 59.36 1 24.24 ? C2 ADP 401 N 1 HETATM 26 N N3 ADP . . . E 5 148.463 27.285 58.936 1 26.18 ? N3 ADP 401 N 1 HETATM 27 C C4 ADP . . . E 5 147.32 26.617 58.721 1 25.16 ? C4 ADP 401 N 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #