data_2O8E # _model_server_result.job_id Lixg81LbeQu-Usnma9VsUA _model_server_result.datetime_utc '2024-11-04 20:33:37' _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 2o8e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":936}' # _entry.id 2O8E # _exptl.entry_id 2O8E _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 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 2O8E _cell.length_a 257.51 _cell.length_b 257.51 _cell.length_c 257.51 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O8E _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 _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 6 _struct_asym.id F _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 C OG SER 676 A SER 676 1_555 E MG MG . A MG 935 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc2 E MG MG . A MG 935 1_555 F O1B ADP . A ADP 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc3 E MG MG . A MG 935 1_555 F O2B ADP . A ADP 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? hydrog WATSON-CRICK hydrog1 A N1 DG 1 E DG 1 1_555 B N3 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 E DG 1 1_555 B O2 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 E DG 1 1_555 B N4 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 2 E DA 2 1_555 B N3 DT 14 F DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 2 E DA 2 1_555 B O4 DT 14 F DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 E DA 3 1_555 B N3 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 E DA 3 1_555 B O4 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 4 E DC 4 1_555 B N1 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 4 E DC 4 1_555 B O6 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 4 E DC 4 1_555 B N2 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 5 E DC 5 1_555 B N1 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 5 E DC 5 1_555 B O6 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 5 E DC 5 1_555 B N2 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 6 E DG 6 1_555 B N3 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 6 E DG 6 1_555 B O2 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 6 E DG 6 1_555 B N4 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DC 7 E DC 7 1_555 B N1 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DC 7 E DC 7 1_555 B O6 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 DC 7 E DC 7 1_555 B N2 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog20 A N1 DG 8 E DG 8 1_555 B O4 DT 8 F DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DG 9 E DG 9 1_555 B N3 DC 7 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N2 DG 9 E DG 9 1_555 B O2 DC 7 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O6 DG 9 E DG 9 1_555 B N4 DC 7 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 10 E DG 10 1_555 B N3 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 10 E DG 10 1_555 B O2 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 10 E DG 10 1_555 B N4 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog27 A N2 DG 10 E DG 10 1_555 B O2 DC 7 F DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N3 DC 11 E DC 11 1_555 B N1 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N4 DC 11 E DC 11 1_555 B O6 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O2 DC 11 E DC 11 1_555 B N2 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N3 DT 12 E DT 12 1_555 B N1 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O4 DT 12 E DT 12 1_555 B N6 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N1 DA 13 E DA 13 1_555 B N3 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N6 DA 13 E DA 13 1_555 B O4 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N1 DG 14 E DG 14 1_555 B N3 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N2 DG 14 E DG 14 1_555 B O2 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A O6 DG 14 E DG 14 1_555 B N4 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog38 A O6 DG 15 E DG 15 1_555 B N4 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 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 2O8E _atom_sites.fract_transf_matrix[1][1] 0.003883 _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] 0.003883 _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] 0.003883 _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 1 MG MG . F 6 ADP A 1 936 2 ADP ADP . G 7 HOH B 1 6 6 HOH HOH . G 7 HOH B 2 11 11 HOH HOH . G 7 HOH B 3 23 23 HOH HOH . G 7 HOH B 4 25 25 HOH HOH . G 7 HOH B 5 26 26 HOH HOH . G 7 HOH B 6 30 30 HOH HOH . G 7 HOH B 7 31 31 HOH HOH . G 7 HOH B 8 34 34 HOH HOH . G 7 HOH B 9 45 45 HOH HOH . G 7 HOH B 10 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 -45.578 -4.058 44.394 1 100.92 ? PB ADP 936 A 1 HETATM 2 O O1B ADP . . . F 6 -46.902 -3.755 43.728 1 100.45 ? O1B ADP 936 A 1 HETATM 3 O O2B ADP . . . F 6 -44.396 -3.82 43.499 1 100.76 ? O2B ADP 936 A 1 HETATM 4 O O3B ADP . . . F 6 -45.515 -5.355 45.17 1 100.42 ? O3B ADP 936 A 1 HETATM 5 P PA ADP . . . F 6 -44.906 -1.458 45.196 1 99.98 ? PA ADP 936 A 1 HETATM 6 O O1A ADP . . . F 6 -43.405 -1.441 45.355 1 99.54 ? O1A ADP 936 A 1 HETATM 7 O O2A ADP . . . F 6 -45.514 -1.065 43.868 1 100.29 ? O2A ADP 936 A 1 HETATM 8 O O3A ADP . . . F 6 -45.424 -2.937 45.545 1 100.44 ? O3A ADP 936 A 1 HETATM 9 O O5' ADP . . . F 6 -45.562 -0.541 46.343 1 98.77 ? O5' ADP 936 A 1 HETATM 10 C C5' ADP . . . F 6 -45.758 0.842 46.06 1 98.45 ? C5' ADP 936 A 1 HETATM 11 C C4' ADP . . . F 6 -45.89 1.673 47.33 1 98.09 ? C4' ADP 936 A 1 HETATM 12 O O4' ADP . . . F 6 -45.35 0.966 48.447 1 98.03 ? O4' ADP 936 A 1 HETATM 13 C C3' ADP . . . F 6 -45.13 2.988 47.204 1 97.84 ? C3' ADP 936 A 1 HETATM 14 O O3' ADP . . . F 6 -46.035 4.093 47.08 1 97.42 ? O3' ADP 936 A 1 HETATM 15 C C2' ADP . . . F 6 -44.296 3.108 48.463 1 97.72 ? C2' ADP 936 A 1 HETATM 16 O O2' ADP . . . F 6 -44.733 4.21 49.256 1 97.74 ? O2' ADP 936 A 1 HETATM 17 C C1' ADP . . . F 6 -44.545 1.833 49.25 1 97.97 ? C1' ADP 936 A 1 HETATM 18 N N9 ADP . . . F 6 -43.258 1.186 49.618 1 98 ? N9 ADP 936 A 1 HETATM 19 C C8 ADP . . . F 6 -42.599 0.27 48.889 1 98.18 ? C8 ADP 936 A 1 HETATM 20 N N7 ADP . . . F 6 -41.455 -0.12 49.508 1 98.38 ? N7 ADP 936 A 1 HETATM 21 C C5 ADP . . . F 6 -41.37 0.558 50.664 1 98.05 ? C5 ADP 936 A 1 HETATM 22 C C6 ADP . . . F 6 -40.414 0.626 51.793 1 97.97 ? C6 ADP 936 A 1 HETATM 23 N N6 ADP . . . F 6 -39.298 -0.139 51.807 1 98.02 ? N6 ADP 936 A 1 HETATM 24 N N1 ADP . . . F 6 -40.702 1.466 52.811 1 98.03 ? N1 ADP 936 A 1 HETATM 25 C C2 ADP . . . F 6 -41.812 2.227 52.814 1 98.04 ? C2 ADP 936 A 1 HETATM 26 N N3 ADP . . . F 6 -42.718 2.217 51.82 1 98.21 ? N3 ADP 936 A 1 HETATM 27 C C4 ADP . . . F 6 -42.558 1.42 50.733 1 98.08 ? C4 ADP 936 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #