data_5WDH # _model_server_result.job_id RVpCEGRXWJzo8c5hlCKc3Q _model_server_result.datetime_utc '2024-11-05 00:21:46' _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 5wdh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5WDH # _exptl.entry_id 5WDH _exptl.method 'X-RAY DIFFRACTION' # _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 5WDH _cell.length_a 63.713 _cell.length_b 63.713 _cell.length_c 242.432 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDH _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _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,D,E,F,G,H,I,J _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 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 metalc ? metalc1 A OG1 THR 130 A THR 417 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 B O2B ADP . A ADP 801 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 C MG MG . A MG 802 1_555 J O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc4 C MG MG . A MG 802 1_555 J O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc5 C MG MG . A MG 802 1_555 J O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc6 C MG MG . A MG 802 1_555 J O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? # _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 5WDH _atom_sites.fract_transf_matrix[1][1] 0.015695 _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] 0.015695 _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] 0.004125 _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 A 1 801 801 ADP ADP . C 3 MG A 1 802 802 MG MG . D 4 UNX A 1 803 1 UNX UNX . E 4 UNX A 1 804 2 UNX UNX . F 4 UNX A 1 805 4 UNX UNX . G 4 UNX A 1 806 6 UNX UNX . H 4 UNX A 1 807 8 UNX UNX . I 4 UNX A 1 808 10 UNX UNX . J 5 HOH A 1 901 1 HOH HOH . J 5 HOH A 2 902 3 HOH HOH . J 5 HOH A 3 903 4 HOH HOH . J 5 HOH A 4 904 2 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 . . . B 2 47.879 30.487 110.959 1 72.53 ? PB ADP 801 A 1 HETATM 2 O O1B ADP . . . B 2 47.014 29.813 109.939 1 57.53 ? O1B ADP 801 A 1 HETATM 3 O O2B ADP . . . B 2 49.323 29.999 110.994 1 72.57 ? O2B ADP 801 A 1 HETATM 4 O O3B ADP . . . B 2 47.726 31.984 111.018 1 68.23 ? O3B ADP 801 A 1 HETATM 5 P PA ADP . . . B 2 47.883 29.135 113.548 1 63 ? PA ADP 801 A 1 HETATM 6 O O1A ADP . . . B 2 48.439 27.799 113.093 1 61.97 ? O1A ADP 801 A 1 HETATM 7 O O2A ADP . . . B 2 48.737 30.139 114.258 1 60.27 ? O2A ADP 801 A 1 HETATM 8 O O3A ADP . . . B 2 47.174 29.918 112.315 1 66.47 ? O3A ADP 801 A 1 HETATM 9 O O5' ADP . . . B 2 46.659 28.788 114.541 1 73.06 ? O5' ADP 801 A 1 HETATM 10 C C5' ADP . . . B 2 45.815 29.761 115.172 1 67.63 ? C5' ADP 801 A 1 HETATM 11 C C4' ADP . . . B 2 45.381 29.147 116.507 1 68.01 ? C4' ADP 801 A 1 HETATM 12 O O4' ADP . . . B 2 44.638 27.95 116.269 1 67.21 ? O4' ADP 801 A 1 HETATM 13 C C3' ADP . . . B 2 46.581 28.722 117.328 1 63.8 ? C3' ADP 801 A 1 HETATM 14 O O3' ADP . . . B 2 46.322 29.047 118.693 1 74.96 ? O3' ADP 801 A 1 HETATM 15 C C2' ADP . . . B 2 46.642 27.215 117.212 1 60.59 ? C2' ADP 801 A 1 HETATM 16 O O2' ADP . . . B 2 47.12 26.657 118.428 1 72.45 ? O2' ADP 801 A 1 HETATM 17 C C1' ADP . . . B 2 45.203 26.839 116.98 1 59.04 ? C1' ADP 801 A 1 HETATM 18 N N9 ADP . . . B 2 45.061 25.655 116.117 1 62.32 ? N9 ADP 801 A 1 HETATM 19 C C8 ADP . . . B 2 45.252 25.682 114.781 1 58.98 ? C8 ADP 801 A 1 HETATM 20 N N7 ADP . . . B 2 45.042 24.462 114.25 1 63.54 ? N7 ADP 801 A 1 HETATM 21 C C5 ADP . . . B 2 44.701 23.62 115.231 1 59.57 ? C5 ADP 801 A 1 HETATM 22 C C6 ADP . . . B 2 44.341 22.187 115.334 1 59.18 ? C6 ADP 801 A 1 HETATM 23 N N6 ADP . . . B 2 44.313 21.381 114.251 1 60.56 ? N6 ADP 801 A 1 HETATM 24 N N1 ADP . . . B 2 44.054 21.692 116.564 1 63.19 ? N1 ADP 801 A 1 HETATM 25 C C2 ADP . . . B 2 44.102 22.478 117.658 1 61.52 ? C2 ADP 801 A 1 HETATM 26 N N3 ADP . . . B 2 44.398 23.789 117.631 1 57.75 ? N3 ADP 801 A 1 HETATM 27 C C4 ADP . . . B 2 44.714 24.414 116.478 1 61.31 ? C4 ADP 801 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #