data_8PMJ # _model_server_result.job_id PbQpQesxsDdZgNXq7VTMsg _model_server_result.datetime_utc '2024-11-04 22:42:36' _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 8pmj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1506}' # _entry.id 8PMJ # _exptl.entry_id 8PMJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 8PMJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PMJ _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id G _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 462 A SER 462 1_555 J MG MG . A MG 1509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc2 A OE1 GLN 503 A GLN 503 1_555 J MG MG . A MG 1509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc3 A OG SER 1120 A SER 1120 1_555 I MG MG . A MG 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 A OE1 GLN 1161 A GLN 1161 1_555 I MG MG . A MG 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc5 B O3G ATP . A ATP 1501 1_555 J MG MG . A MG 1509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc6 G O3B ADP . A ADP 1506 1_555 H V VO4 . A VO4 1507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc7 G O1B ADP . A ADP 1506 1_555 I MG MG . A MG 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc8 H O1 VO4 . A VO4 1507 1_555 I MG MG . A MG 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc9 I MG MG . A MG 1508 1_555 K O HOH . A HOH 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc10 J MG MG . A MG 1509 1_555 K O HOH . A HOH 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc11 J MG MG . A MG 1509 1_555 K O HOH . A HOH 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? # _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 8PMJ _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 B 2 ATP A 1 1501 1501 ATP ATP . C 3 CLR A 1 1502 1601 CLR CLR . D 3 CLR A 1 1503 1701 CLR CLR . E 3 CLR A 1 1504 1801 CLR CLR . F 3 CLR A 1 1505 1901 CLR CLR . G 4 ADP A 1 1506 1902 ADP ADP . H 5 VO4 A 1 1507 1903 VO4 VO4 . I 6 MG A 1 1508 1303 MG MG . J 6 MG A 1 1509 1 MG MG . K 7 HOH A 1 1601 3 HOH HOH . K 7 HOH A 2 1602 1 HOH HOH . K 7 HOH A 3 1603 4 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 P PB ADP . . . G 4 162.349 93.755 172.93 1 20 ? PB ADP 1506 A 1 HETATM 2 O O1B ADP . . . G 4 160.873 93.805 172.956 1 20 ? O1B ADP 1506 A 1 HETATM 3 O O2B ADP . . . G 4 162.888 92.398 173.088 1 20 ? O2B ADP 1506 A 1 HETATM 4 O O3B ADP . . . G 4 162.97 94.716 173.841 1 20 ? O3B ADP 1506 A 1 HETATM 5 P PA ADP . . . G 4 162.184 94.316 170.05 1 20 ? PA ADP 1506 A 1 HETATM 6 O O1A ADP . . . G 4 161.314 93.146 169.769 1 20 ? O1A ADP 1506 A 1 HETATM 7 O O2A ADP . . . G 4 161.624 95.67 169.826 1 20 ? O2A ADP 1506 A 1 HETATM 8 O O3A ADP . . . G 4 162.803 94.271 171.513 1 20 ? O3A ADP 1506 A 1 HETATM 9 O O5' ADP . . . G 4 163.572 94.159 169.286 1 20 ? O5' ADP 1506 A 1 HETATM 10 C C5' ADP . . . G 4 163.564 93.907 167.877 1 20 ? C5' ADP 1506 A 1 HETATM 11 C C4' ADP . . . G 4 164.706 94.659 167.256 1 20 ? C4' ADP 1506 A 1 HETATM 12 O O4' ADP . . . G 4 164.249 95.202 166.001 1 20 ? O4' ADP 1506 A 1 HETATM 13 C C3' ADP . . . G 4 165.204 95.879 168.023 1 20 ? C3' ADP 1506 A 1 HETATM 14 O O3' ADP . . . G 4 166.523 96.19 167.612 1 20 ? O3' ADP 1506 A 1 HETATM 15 C C2' ADP . . . G 4 164.223 96.958 167.57 1 20 ? C2' ADP 1506 A 1 HETATM 16 O O2' ADP . . . G 4 164.795 98.241 167.625 1 20 ? O2' ADP 1506 A 1 HETATM 17 C C1' ADP . . . G 4 163.959 96.572 166.124 1 20 ? C1' ADP 1506 A 1 HETATM 18 N N9 ADP . . . G 4 162.587 96.748 165.684 1 20 ? N9 ADP 1506 A 1 HETATM 19 C C8 ADP . . . G 4 161.453 96.596 166.432 1 20 ? C8 ADP 1506 A 1 HETATM 20 N N7 ADP . . . G 4 160.355 96.794 165.753 1 20 ? N7 ADP 1506 A 1 HETATM 21 C C5 ADP . . . G 4 160.794 97.098 164.477 1 20 ? C5 ADP 1506 A 1 HETATM 22 C C6 ADP . . . G 4 160.107 97.415 163.293 1 20 ? C6 ADP 1506 A 1 HETATM 23 N N6 ADP . . . G 4 158.785 97.468 163.205 1 20 ? N6 ADP 1506 A 1 HETATM 24 N N1 ADP . . . G 4 160.844 97.669 162.191 1 20 ? N1 ADP 1506 A 1 HETATM 25 C C2 ADP . . . G 4 162.176 97.608 162.286 1 20 ? C2 ADP 1506 A 1 HETATM 26 N N3 ADP . . . G 4 162.929 97.321 163.341 1 20 ? N3 ADP 1506 A 1 HETATM 27 C C4 ADP . . . G 4 162.17 97.069 164.419 1 20 ? C4 ADP 1506 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #