data_8RU0 # _model_server_result.job_id vPvlzFtvJrR0srVFyvcVuw _model_server_result.datetime_utc '2024-11-23 02:21:43' _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 8ru0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8RU0 # _exptl.entry_id 8RU0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 8RU0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RU0 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 2 E N N ? 2 H N N ? 2 K 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 covale ? covale1 A C GLU 72 B GLU 72 1_555 A N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C HIC 73 B HIC 73 1_555 A N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C GLU 72 A GLU 72 1_555 B N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C HIC 73 A HIC 73 1_555 B N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 F MG MG . B MG 402 1_555 G O2 PO4 . B PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 H O1B ADP . A ADP 401 1_555 I MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc3 I MG MG . A MG 402 1_555 J O2 PO4 . A PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc4 K O1B ADP . C ADP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc5 L MG MG . C MG 402 1_555 M O2 PO4 . C PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc6 N MG MG . D MG 401 1_555 O O1B ATP . D ATP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc7 N MG MG . D MG 401 1_555 O O1G ATP . D ATP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? # _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 8RU0 _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 E 2 ADP B 1 401 401 ADP ADP . F 3 MG B 1 402 402 MG MG . G 4 PO4 B 1 403 403 PO4 PO4 . H 2 ADP A 1 401 401 ADP ADP . I 3 MG A 1 402 402 MG MG . J 4 PO4 A 1 403 403 PO4 PO4 . K 2 ADP C 1 401 401 ADP ADP . L 3 MG C 1 402 402 MG MG . M 4 PO4 C 1 403 403 PO4 PO4 . N 3 MG D 1 401 402 MG MG . O 5 ATP D 1 402 403 ATP ATP . # 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 2 154.066 148.615 189.309 1 64.81 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . E 2 153.909 149.878 188.502 1 62.09 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . E 2 153.629 147.369 188.577 1 76.02 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . E 2 155.39 148.502 190.025 1 62.71 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . E 2 151.407 148.669 190.191 1 56.71 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . E 2 151.204 149.013 188.736 1 56.71 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . E 2 150.904 147.351 190.726 1 74.68 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . E 2 152.985 148.764 190.494 1 60.35 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . E 2 150.809 149.846 191.112 1 70.45 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . E 2 151.692 150.662 191.877 1 66.23 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . E 2 150.996 151.935 192.348 1 62.62 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . E 2 149.622 151.964 191.957 1 68.62 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . E 2 151.014 152.068 193.862 1 61.82 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . E 2 152.019 153.002 194.264 1 68.8 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . E 2 149.642 152.592 194.236 1 66.03 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . E 2 149.765 153.875 194.852 1 74.65 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . E 2 148.882 152.71 192.925 1 59.82 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . E 2 147.503 152.182 193.078 1 56.82 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . E 2 147.159 150.888 193.21 1 63.51 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . E 2 145.814 150.749 193.333 1 62.27 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . E 2 145.275 151.98 193.283 1 57.97 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . E 2 143.91 152.553 193.352 1 62.52 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . E 2 142.824 151.758 193.505 1 66.22 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . E 2 143.785 153.894 193.258 1 58.44 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . E 2 144.855 154.695 193.106 1 56.86 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . E 2 146.119 154.244 193.035 1 56.9 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . E 2 146.392 152.921 193.117 1 54.19 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #