data_8COG # _model_server_result.job_id zbl5oYJuSocxWoIGRzzyYA _model_server_result.datetime_utc '2024-10-11 03:22:46' _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 8cog # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8COG # _exptl.entry_id 8COG _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 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 8COG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8COG _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_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 216 F CYS 216 1_555 A SG CYS 256 F CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? covale ? covale1 A C GLU 71 F GLU 71 1_555 A N HIC 72 F HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C HIC 72 F HIC 72 1_555 A N GLY 73 F GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 B O2B ADP . F ADP 401 1_555 C MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _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 8COG _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 ADP F 1 401 401 ADP ADP . C 3 MG F 1 402 402 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 . . . B 2 133.761 121.69 145.929 1 30.26 ? PB ADP 401 F 1 HETATM 2 O O1B ADP . . . B 2 132.712 121.89 144.874 1 36.76 ? O1B ADP 401 F 1 HETATM 3 O O2B ADP . . . B 2 133.231 120.866 147.057 1 38.91 ? O2B ADP 401 F 1 HETATM 4 O O3B ADP . . . B 2 134.434 122.976 146.359 1 25.69 ? O3B ADP 401 F 1 HETATM 5 P PA ADP . . . B 2 136.133 120.021 145.918 1 28.91 ? PA ADP 401 F 1 HETATM 6 O O1A ADP . . . B 2 135.833 118.57 145.953 1 36.17 ? O1A ADP 401 F 1 HETATM 7 O O2A ADP . . . B 2 136.511 120.652 147.213 1 33.95 ? O2A ADP 401 F 1 HETATM 8 O O3A ADP . . . B 2 134.839 120.71 145.302 1 28.24 ? O3A ADP 401 F 1 HETATM 9 O O5' ADP . . . B 2 137.261 120.312 144.804 1 32.62 ? O5' ADP 401 F 1 HETATM 10 C C5' ADP . . . B 2 137.047 121.143 143.604 1 33.39 ? C5' ADP 401 F 1 HETATM 11 C C4' ADP . . . B 2 138.148 122.17 143.486 1 31.52 ? C4' ADP 401 F 1 HETATM 12 O O4' ADP . . . B 2 139.381 121.458 143.684 1 30.33 ? O4' ADP 401 F 1 HETATM 13 C C3' ADP . . . B 2 138.332 122.888 142.14 1 34.83 ? C3' ADP 401 F 1 HETATM 14 O O3' ADP . . . B 2 138.095 124.287 142.239 1 37.92 ? O3' ADP 401 F 1 HETATM 15 C C2' ADP . . . B 2 139.825 122.783 141.77 1 33.11 ? C2' ADP 401 F 1 HETATM 16 O O2' ADP . . . B 2 140.477 124.051 141.752 1 31.45 ? O2' ADP 401 F 1 HETATM 17 C C1' ADP . . . B 2 140.429 121.916 142.864 1 26.26 ? C1' ADP 401 F 1 HETATM 18 N N9 ADP . . . B 2 141.14 120.717 142.447 1 22.67 ? N9 ADP 401 F 1 HETATM 19 C C8 ADP . . . B 2 140.574 119.54 142.03 1 22.8 ? C8 ADP 401 F 1 HETATM 20 N N7 ADP . . . B 2 141.437 118.566 141.857 1 24.26 ? N7 ADP 401 F 1 HETATM 21 C C5 ADP . . . B 2 142.654 119.135 142.181 1 23.3 ? C5 ADP 401 F 1 HETATM 22 C C6 ADP . . . B 2 143.962 118.603 142.181 1 25.64 ? C6 ADP 401 F 1 HETATM 23 N N6 ADP . . . B 2 144.23 117.33 141.882 1 24.43 ? N6 ADP 401 F 1 HETATM 24 N N1 ADP . . . B 2 144.974 119.451 142.542 1 29.63 ? N1 ADP 401 F 1 HETATM 25 C C2 ADP . . . B 2 144.669 120.737 142.847 1 28.84 ? C2 ADP 401 F 1 HETATM 26 N N3 ADP . . . B 2 143.468 121.325 142.922 1 25.04 ? N3 ADP 401 F 1 HETATM 27 C C4 ADP . . . B 2 142.488 120.466 142.555 1 23.1 ? C4 ADP 401 F 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #