data_2O8C # _model_server_result.job_id n04q3vPW2yQDe8z7YQOb7g _model_server_result.datetime_utc '2025-02-18 12:57:16' _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 2o8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":936}' # _entry.id 2O8C # _exptl.entry_id 2O8C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 2O8C _cell.length_a 259.81 _cell.length_b 259.81 _cell.length_c 259.81 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O8C _symmetry.cell_setting ? _symmetry.Int_Tables_number 212 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 H 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 O3' DC 7 E DC 7 1_555 A P 6OG 8 E 6OG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale2 A O3' 6OG 8 E 6OG 8 1_555 A P DC 9 E DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? metalc ? metalc1 C OG SER 676 A SER 676 1_555 E MG MG . A MG 935 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc2 E MG MG . A MG 935 1_555 F O1B ADP . A ADP 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc3 G MG MG . B MG 102 1_555 H O2B ADP . B ADP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? metalc ? metalc4 G MG MG . B MG 102 1_555 H O3B ADP . B ADP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc5 G MG MG . B MG 102 1_555 D OG SER 803 B SER 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? hydrog 'DG-DC PAIR' hydrog1 A N2 DG 1 E DG 1 1_555 B O2 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DA 3 E DA 3 1_555 B N3 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N6 DA 3 E DA 3 1_555 B O4 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog4 A O2 DC 4 E DC 4 1_555 B N1 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N3 DC 5 E DC 5 1_555 B N1 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N4 DC 5 E DC 5 1_555 B O6 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O2 DC 5 E DC 5 1_555 B N2 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DG 6 E DG 6 1_555 B N3 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N2 DG 6 E DG 6 1_555 B O2 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O6 DG 6 E DG 6 1_555 B N4 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 7 E DC 7 1_555 B N1 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 7 E DC 7 1_555 B O6 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 7 E DC 7 1_555 B N2 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog '6OG-DT MISPAIR' hydrog14 A N1 6OG 8 E 6OG 8 1_555 B O4 DT 8 F DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 9 E DC 9 1_555 B N1 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 9 E DC 9 1_555 B O6 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 9 E DC 9 1_555 B N2 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 DG 10 E DG 10 1_555 B N3 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 DG 10 E DG 10 1_555 B O2 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 DG 10 E DG 10 1_555 B N4 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 11 E DC 11 1_555 B N1 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 11 E DC 11 1_555 B O6 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 11 E DC 11 1_555 B N2 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog24 A N3 DT 12 E DT 12 1_555 B N1 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog25 A N1 DA 13 E DA 13 1_555 B N3 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog26 A N2 DG 14 E DG 14 1_555 B O2 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog27 A N1 DG 15 E DG 15 1_555 B N3 DC 1 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 43 n n PB O2B ADP sing 44 n n PB O3B ADP sing 45 n n PB O3A ADP sing 46 n n O2B HOB2 ADP sing 47 n n O3B HOB3 ADP sing 48 n n PA O1A ADP doub 49 n n PA O2A ADP sing 50 n n PA O3A ADP sing 51 n n PA O5' ADP sing 52 n n O2A HOA2 ADP sing 53 n n O5' C5' ADP sing 54 n n C5' C4' ADP sing 55 n n C5' "H5'1" ADP sing 56 n n C5' "H5'2" ADP sing 57 n n C4' O4' ADP sing 58 n n C4' C3' ADP sing 59 n n C4' H4' ADP sing 60 n n O4' C1' ADP sing 61 n n C3' O3' ADP sing 62 n n C3' C2' ADP sing 63 n n C3' H3' ADP sing 64 n n O3' HO3' ADP sing 65 n n C2' O2' ADP sing 66 n n C2' C1' ADP sing 67 n n C2' H2' ADP sing 68 n n O2' HO2' ADP sing 69 n n C1' N9 ADP sing 70 n n C1' H1' ADP sing 71 n n N9 C8 ADP sing 72 n y N9 C4 ADP sing 73 n y C8 N7 ADP doub 74 n y C8 H8 ADP sing 75 n n N7 C5 ADP sing 76 n y C5 C6 ADP sing 77 n y C5 C4 ADP doub 78 n y C6 N6 ADP sing 79 n n C6 N1 ADP doub 80 n y N6 HN61 ADP sing 81 n n N6 HN62 ADP sing 82 n n N1 C2 ADP sing 83 n y C2 N3 ADP doub 84 n y C2 H2 ADP sing 85 n n N3 C4 ADP sing 86 n y # _atom_sites.entry_id 2O8C _atom_sites.fract_transf_matrix[1][1] 0.003849 _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] 0.003849 _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] 0.003849 _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 5 MG A 1 935 101 MG MG . F 6 ADP A 1 936 201 ADP ADP . G 5 MG B 1 102 102 MG MG . H 6 ADP B 1 202 202 ADP ADP . I 7 HOH F 1 13 13 HOH HOH . J 7 HOH A 1 937 50 HOH HOH . K 7 HOH B 1 1 1 HOH HOH . K 7 HOH B 2 2 2 HOH HOH . K 7 HOH B 3 6 6 HOH HOH . K 7 HOH B 4 8 8 HOH HOH . K 7 HOH B 5 9 9 HOH HOH . K 7 HOH B 6 10 10 HOH HOH . K 7 HOH B 7 12 12 HOH HOH . K 7 HOH B 8 14 14 HOH HOH . K 7 HOH B 9 16 16 HOH HOH . K 7 HOH B 10 18 18 HOH HOH . K 7 HOH B 11 19 19 HOH HOH . K 7 HOH B 12 23 23 HOH HOH . K 7 HOH B 13 25 25 HOH HOH . K 7 HOH B 14 30 30 HOH HOH . K 7 HOH B 15 31 31 HOH HOH . K 7 HOH B 16 37 37 HOH HOH . K 7 HOH B 17 40 40 HOH HOH . K 7 HOH B 18 45 45 HOH HOH . K 7 HOH B 19 46 46 HOH HOH . K 7 HOH B 20 47 47 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 . . . F 6 -45.846 -4.285 45.36 1 75.65 ? PB ADP 936 A 1 HETATM 2 O O1B ADP . . . F 6 -45.305 -3.887 44.005 1 75.55 ? O1B ADP 936 A 1 HETATM 3 O O2B ADP . . . F 6 -44.931 -5.164 46.172 1 75.48 ? O2B ADP 936 A 1 HETATM 4 O O3B ADP . . . F 6 -47.274 -4.777 45.322 1 75.53 ? O3B ADP 936 A 1 HETATM 5 P PA ADP . . . F 6 -44.996 -1.623 45.86 1 74.95 ? PA ADP 936 A 1 HETATM 6 O O1A ADP . . . F 6 -43.543 -2.041 45.817 1 74.72 ? O1A ADP 936 A 1 HETATM 7 O O2A ADP . . . F 6 -45.602 -0.964 44.642 1 75.13 ? O2A ADP 936 A 1 HETATM 8 O O3A ADP . . . F 6 -45.897 -2.916 46.224 1 75.33 ? O3A ADP 936 A 1 HETATM 9 O O5' ADP . . . F 6 -45.214 -0.642 47.125 1 73.65 ? O5' ADP 936 A 1 HETATM 10 C C5' ADP . . . F 6 -46.495 -0.084 47.416 1 72.26 ? C5' ADP 936 A 1 HETATM 11 C C4' ADP . . . F 6 -46.382 1.182 48.27 1 71.53 ? C4' ADP 936 A 1 HETATM 12 O O4' ADP . . . F 6 -45.754 0.912 49.527 1 70.94 ? O4' ADP 936 A 1 HETATM 13 C C3' ADP . . . F 6 -45.584 2.29 47.596 1 71.23 ? C3' ADP 936 A 1 HETATM 14 O O3' ADP . . . F 6 -46.455 3.355 47.202 1 71.44 ? O3' ADP 936 A 1 HETATM 15 C C2' ADP . . . F 6 -44.606 2.802 48.635 1 70.76 ? C2' ADP 936 A 1 HETATM 16 O O2' ADP . . . F 6 -44.855 4.183 48.907 1 70.55 ? O2' ADP 936 A 1 HETATM 17 C C1' ADP . . . F 6 -44.85 1.964 49.882 1 70.43 ? C1' ADP 936 A 1 HETATM 18 N N9 ADP . . . F 6 -43.58 1.378 50.377 1 70.24 ? N9 ADP 936 A 1 HETATM 19 C C8 ADP . . . F 6 -42.81 0.498 49.711 1 70.3 ? C8 ADP 936 A 1 HETATM 20 N N7 ADP . . . F 6 -41.717 0.146 50.433 1 70.34 ? N7 ADP 936 A 1 HETATM 21 C C5 ADP . . . F 6 -41.778 0.812 51.599 1 70.22 ? C5 ADP 936 A 1 HETATM 22 C C6 ADP . . . F 6 -40.943 0.898 52.822 1 70.17 ? C6 ADP 936 A 1 HETATM 23 N N6 ADP . . . F 6 -39.797 0.188 52.945 1 70.2 ? N6 ADP 936 A 1 HETATM 24 N N1 ADP . . . F 6 -41.368 1.714 53.811 1 70.25 ? N1 ADP 936 A 1 HETATM 25 C C2 ADP . . . F 6 -42.508 2.427 53.705 1 70.31 ? C2 ADP 936 A 1 HETATM 26 N N3 ADP . . . F 6 -43.315 2.397 52.627 1 70.19 ? N3 ADP 936 A 1 HETATM 27 C C4 ADP . . . F 6 -43.008 1.623 51.557 1 70.18 ? C4 ADP 936 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #