data_4BGD # _model_server_result.job_id oEfZSIeUxv1LAFJYq4olmw _model_server_result.datetime_utc '2024-11-23 21:41:42' _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 4bgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3164}' # _entry.id 4BGD # _exptl.entry_id 4BGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 4BGD _cell.length_a 107.64 _cell.length_b 178.64 _cell.length_c 180.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 F O HOH . A HOH 3007 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc2 F O HOH . A HOH 3008 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 F O HOH . A HOH 3009 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc4 F O HOH . A HOH 3011 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc5 F O HOH . A HOH 3012 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc6 C O3B ADP . A ADP 3164 1_555 D MG MG . A MG 3165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? # _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 4BGD _atom_sites.fract_transf_matrix[1][1] 0.00929 _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] 0.005598 _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] 0.005543 _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 C 3 ADP A 1 3164 3164 ADP ADP . D 4 MG A 1 3165 3165 MG MG . E 5 PE5 A 1 3166 3166 PE5 PE5 . F 6 HOH A 1 3001 3001 HOH HOH . F 6 HOH A 2 3002 3002 HOH HOH . F 6 HOH A 3 3003 3003 HOH HOH . F 6 HOH A 4 3004 3004 HOH HOH . F 6 HOH A 5 3005 3005 HOH HOH . F 6 HOH A 6 3006 3006 HOH HOH . F 6 HOH A 7 3007 3007 HOH HOH . F 6 HOH A 8 3008 3008 HOH HOH . F 6 HOH A 9 3009 3009 HOH HOH . F 6 HOH A 10 3010 3010 HOH HOH . F 6 HOH A 11 3011 3011 HOH HOH . F 6 HOH A 12 3012 3012 HOH HOH . F 6 HOH A 13 3013 3013 HOH HOH . F 6 HOH A 14 3014 3014 HOH HOH . G 6 HOH C 1 3001 3001 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 . . . C 3 107.02 -0.481 47.573 1 106.08 ? PB ADP 3164 A 1 HETATM 2 O O1B ADP . . . C 3 105.768 -0.088 46.856 1 98.46 ? O1B ADP 3164 A 1 HETATM 3 O O2B ADP . . . C 3 106.886 -0.725 49.06 1 87.08 ? O2B ADP 3164 A 1 HETATM 4 O O3B ADP . . . C 3 107.846 -1.442 46.75 1 89.91 ? O3B ADP 3164 A 1 HETATM 5 P PA ADP . . . C 3 108.663 1.361 46.286 1 106.57 ? PA ADP 3164 A 1 HETATM 6 O O1A ADP . . . C 3 107.587 1.881 45.365 1 116.23 ? O1A ADP 3164 A 1 HETATM 7 O O2A ADP . . . C 3 109.574 0.253 45.838 1 90.63 ? O2A ADP 3164 A 1 HETATM 8 O O3A ADP . . . C 3 107.892 0.871 47.609 1 110.2 ? O3A ADP 3164 A 1 HETATM 9 O O5' ADP . . . C 3 109.528 2.62 46.801 1 106.61 ? O5' ADP 3164 A 1 HETATM 10 C C5' ADP . . . C 3 108.908 3.837 47.266 1 118.34 ? C5' ADP 3164 A 1 HETATM 11 C C4' ADP . . . C 3 109.63 5.106 46.786 1 115.53 ? C4' ADP 3164 A 1 HETATM 12 O O4' ADP . . . C 3 110.58 5.556 47.762 1 124.07 ? O4' ADP 3164 A 1 HETATM 13 C C3' ADP . . . C 3 110.448 4.9 45.518 1 109.25 ? C3' ADP 3164 A 1 HETATM 14 O O3' ADP . . . C 3 110.594 6.129 44.813 1 100.45 ? O3' ADP 3164 A 1 HETATM 15 C C2' ADP . . . C 3 111.828 4.547 45.981 1 111 ? C2' ADP 3164 A 1 HETATM 16 O O2' ADP . . . C 3 112.711 4.834 44.898 1 98.58 ? O2' ADP 3164 A 1 HETATM 17 C C1' ADP . . . C 3 111.923 5.445 47.22 1 124.09 ? C1' ADP 3164 A 1 HETATM 18 N N9 ADP . . . C 3 112.835 4.981 48.304 1 127.24 ? N9 ADP 3164 A 1 HETATM 19 C C8 ADP . . . C 3 113.069 3.719 48.696 1 138.91 ? C8 ADP 3164 A 1 HETATM 20 N N7 ADP . . . C 3 113.947 3.697 49.733 1 145.74 ? N7 ADP 3164 A 1 HETATM 21 C C5 ADP . . . C 3 114.285 4.961 50.016 1 136.42 ? C5 ADP 3164 A 1 HETATM 22 C C6 ADP . . . C 3 115.17 5.647 50.982 1 141.4 ? C6 ADP 3164 A 1 HETATM 23 N N6 ADP . . . C 3 115.887 4.945 51.887 1 145.23 ? N6 ADP 3164 A 1 HETATM 24 N N1 ADP . . . C 3 115.24 6.997 50.934 1 135.66 ? N1 ADP 3164 A 1 HETATM 25 C C2 ADP . . . C 3 114.535 7.715 50.042 1 128.74 ? C2 ADP 3164 A 1 HETATM 26 N N3 ADP . . . C 3 113.716 7.144 49.14 1 125.73 ? N3 ADP 3164 A 1 HETATM 27 C C4 ADP . . . C 3 113.547 5.802 49.076 1 128.3 ? C4 ADP 3164 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #