data_7NG4 # _model_server_result.job_id 1hq5cClG7YYKRe2-BQ7Vgw _model_server_result.datetime_utc '2024-11-22 22:26:50' _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 7ng4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1001}' # _entry.id 7NG4 # _exptl.entry_id 7NG4 _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 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 90 _cell.entry_id 7NG4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NG4 _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 PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,H,I,J,K,L,M,N,O,P,Q _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 N N N ? 5 O 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 OG1 THR 424 A THR 530 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc2 H O1G ATP . A ATP 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc3 H O2G ATP . A ATP 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc4 H O1B ATP . A ATP 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc5 H O1A ATP . A ATP 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc6 B OG1 THR 424 B THR 530 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc7 J O1G ATP . B ATP 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc8 J O2G ATP . B ATP 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc9 J O1B ATP . B ATP 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc10 C OG1 THR 424 C THR 530 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc11 L O1G ATP . C ATP 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc12 L O2G ATP . C ATP 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc13 L O1B ATP . C ATP 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc14 L O1A ATP . C ATP 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc15 F OG1 THR 424 F THR 530 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc16 P O1G ATP . F ATP 1001 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc17 P O2G ATP . F ATP 1001 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc18 P O1B ATP . F ATP 1001 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc19 P O3B ATP . F ATP 1001 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc20 P O1A ATP . F ATP 1001 1_555 Q MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? # _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 7NG4 _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 H 3 ATP A 1 1001 1001 ATP ATP . I 4 MG A 1 1002 1002 MG MG . J 3 ATP B 1 1001 1001 ATP ATP . K 4 MG B 1 1002 1002 MG MG . L 3 ATP C 1 1001 1001 ATP ATP . M 4 MG C 1 1002 1002 MG MG . N 5 ADP D 1 1001 1001 ADP ADP . O 5 ADP E 1 1001 1001 ADP ADP . P 3 ATP F 1 1001 1001 ATP ATP . Q 4 MG F 1 1002 1002 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 P PB ADP . . . N 5 213.72 187.732 231.405 1 195.39 ? PB ADP 1001 D 1 HETATM 2 O O1B ADP . . . N 5 213.632 186.805 230.225 1 195.39 ? O1B ADP 1001 D 1 HETATM 3 O O2B ADP . . . N 5 214.139 187.039 232.666 1 195.39 ? O2B ADP 1001 D 1 HETATM 4 O O3B ADP . . . N 5 212.599 188.723 231.514 1 195.39 ? O3B ADP 1001 D 1 HETATM 5 P PA ADP . . . N 5 215.321 188.762 229.604 1 195.39 ? PA ADP 1001 D 1 HETATM 6 O O1A ADP . . . N 5 214.043 189.199 228.956 1 195.39 ? O1A ADP 1001 D 1 HETATM 7 O O2A ADP . . . N 5 215.976 187.456 229.202 1 195.39 ? O2A ADP 1001 D 1 HETATM 8 O O3A ADP . . . N 5 214.988 188.629 231.135 1 195.39 ? O3A ADP 1001 D 1 HETATM 9 O O5' ADP . . . N 5 216.398 189.939 229.532 1 195.39 ? O5' ADP 1001 D 1 HETATM 10 C C5' ADP . . . N 5 217.079 190.375 230.705 1 195.39 ? C5' ADP 1001 D 1 HETATM 11 C C4' ADP . . . N 5 218.471 190.928 230.418 1 195.39 ? C4' ADP 1001 D 1 HETATM 12 O O4' ADP . . . N 5 219.364 190.626 231.492 1 195.39 ? O4' ADP 1001 D 1 HETATM 13 C C3' ADP . . . N 5 219.132 190.352 229.167 1 195.39 ? C3' ADP 1001 D 1 HETATM 14 O O3' ADP . . . N 5 219.185 191.37 228.165 1 195.39 ? O3' ADP 1001 D 1 HETATM 15 C C2' ADP . . . N 5 220.495 189.873 229.589 1 195.39 ? C2' ADP 1001 D 1 HETATM 16 O O2' ADP . . . N 5 221.582 190.311 228.774 1 195.39 ? O2' ADP 1001 D 1 HETATM 17 C C1' ADP . . . N 5 220.678 190.446 230.965 1 195.39 ? C1' ADP 1001 D 1 HETATM 18 N N9 ADP . . . N 5 221.48 189.532 231.801 1 195.39 ? N9 ADP 1001 D 1 HETATM 19 C C8 ADP . . . N 5 221.265 189.401 233.106 1 195.39 ? C8 ADP 1001 D 1 HETATM 20 N N7 ADP . . . N 5 222.111 188.505 233.666 1 195.39 ? N7 ADP 1001 D 1 HETATM 21 C C5 ADP . . . N 5 222.892 188.045 232.69 1 195.39 ? C5 ADP 1001 D 1 HETATM 22 C C6 ADP . . . N 5 223.992 187.08 232.609 1 195.39 ? C6 ADP 1001 D 1 HETATM 23 N N6 ADP . . . N 5 224.429 186.422 233.702 1 195.39 ? N6 ADP 1001 D 1 HETATM 24 N N1 ADP . . . N 5 224.536 186.886 231.402 1 195.39 ? N1 ADP 1001 D 1 HETATM 25 C C2 ADP . . . N 5 224.106 187.534 230.306 1 195.39 ? C2 ADP 1001 D 1 HETATM 26 N N3 ADP . . . N 5 223.114 188.424 230.316 1 195.39 ? N3 ADP 1001 D 1 HETATM 27 C C4 ADP . . . N 5 222.479 188.721 231.46 1 195.39 ? C4 ADP 1001 D 1 HETATM 28 H "H5'1" ADP . . . N 5 217.211 189.6 231.441 1 195.39 ? "H5'1" ADP 1001 D 1 HETATM 29 H "H5'2" ADP . . . N 5 216.486 191.162 231.175 1 195.39 ? "H5'2" ADP 1001 D 1 HETATM 30 H H4' ADP . . . N 5 218.396 192.019 230.301 1 195.39 ? H4' ADP 1001 D 1 HETATM 31 H H3' ADP . . . N 5 218.643 189.456 228.793 1 195.39 ? H3' ADP 1001 D 1 HETATM 32 H HO3' ADP . . . N 5 219.576 191.027 227.351 1 195.39 ? HO3' ADP 1001 D 1 HETATM 33 H H2' ADP . . . N 5 220.422 188.775 229.591 1 195.39 ? H2' ADP 1001 D 1 HETATM 34 H HO2' ADP . . . N 5 221.53 189.895 227.903 1 195.39 ? HO2' ADP 1001 D 1 HETATM 35 H H1' ADP . . . N 5 221.186 191.417 230.882 1 195.39 ? H1' ADP 1001 D 1 HETATM 36 H H8 ADP . . . N 5 220.502 189.942 233.637 1 195.39 ? H8 ADP 1001 D 1 HETATM 37 H HN61 ADP . . . N 5 224.002 186.591 234.597 1 195.39 ? HN61 ADP 1001 D 1 HETATM 38 H HN62 ADP . . . N 5 225.183 185.761 233.621 1 195.39 ? HN62 ADP 1001 D 1 HETATM 39 H H2 ADP . . . N 5 224.596 187.336 229.365 1 195.39 ? H2 ADP 1001 D 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 84 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #