data_7S5Y # _model_server_result.job_id aE9UvHHdNc8wLbVN7da4zQ _model_server_result.datetime_utc '2024-12-26 10:44:07' _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 7s5y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1601}' # _entry.id 7S5Y # _exptl.entry_id 7S5Y _exptl.method 'ELECTRON MICROSCOPY' # _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 7S5Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7S5Y _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 3 _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 disulf ? disulf1 E SG CYS 7 E CYS 7 1_555 E SG CYS 27 E CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 E OE1 GLN 775 E GLN 775 1_555 G MG MG . E MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc2 E OG SER 1386 E SER 1386 1_555 H MG MG . E MG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc3 F O1B ADP . E ADP 1601 1_555 H MG MG . E MG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc4 F O2B ADP . E ADP 1601 1_555 H MG MG . E MG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc5 F O3A ADP . E ADP 1601 1_555 H MG MG . E MG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc6 G MG MG . E MG 1602 1_555 I O2G ATP . E ATP 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc7 G MG MG . E MG 1602 1_555 I O3B ATP . E ATP 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc8 G MG MG . E MG 1602 1_555 I O3G ATP . E ATP 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc9 G MG MG . E MG 1602 1_555 I O2B ATP . E ATP 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _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 7S5Y _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 F 3 ADP E 1 1601 2002 ADP ADP . G 4 MG E 1 1602 2003 MG MG . H 4 MG E 1 1603 2004 MG MG . I 5 ATP E 1 1604 2005 ATP ATP . # 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 3 182.831 288.051 281.775 1 177.95 ? PB ADP 1601 E 1 HETATM 2 O O1B ADP . . . F 3 181.819 289.14 281.582 1 177.95 ? O1B ADP 1601 E 1 HETATM 3 O O2B ADP . . . F 3 184.178 288.565 282.204 1 177.95 ? O2B ADP 1601 E 1 HETATM 4 O O3B ADP . . . F 3 182.32 286.874 282.563 1 177.95 ? O3B ADP 1601 E 1 HETATM 5 P PA ADP . . . F 3 182.007 286.749 279.39 1 177.95 ? PA ADP 1601 E 1 HETATM 6 O O1A ADP . . . F 3 182.263 287.174 277.97 1 177.95 ? O1A ADP 1601 E 1 HETATM 7 O O2A ADP . . . F 3 180.627 287 279.931 1 177.95 ? O2A ADP 1601 E 1 HETATM 8 O O3A ADP . . . F 3 183.111 287.492 280.294 1 177.95 ? O3A ADP 1601 E 1 HETATM 9 O O5' ADP . . . F 3 182.354 285.187 279.478 1 177.95 ? O5' ADP 1601 E 1 HETATM 10 C C5' ADP . . . F 3 181.751 284.311 280.419 1 177.95 ? C5' ADP 1601 E 1 HETATM 11 C C4' ADP . . . F 3 182.124 282.916 279.957 1 177.95 ? C4' ADP 1601 E 1 HETATM 12 O O4' ADP . . . F 3 181.657 282.747 278.621 1 177.95 ? O4' ADP 1601 E 1 HETATM 13 C C3' ADP . . . F 3 183.633 282.758 279.93 1 177.95 ? C3' ADP 1601 E 1 HETATM 14 O O3' ADP . . . F 3 184.046 281.785 280.889 1 177.95 ? O3' ADP 1601 E 1 HETATM 15 C C2' ADP . . . F 3 183.985 282.274 278.541 1 177.95 ? C2' ADP 1601 E 1 HETATM 16 O O2' ADP . . . F 3 184.602 280.988 278.613 1 177.95 ? O2' ADP 1601 E 1 HETATM 17 C C1' ADP . . . F 3 182.671 282.174 277.797 1 177.95 ? C1' ADP 1601 E 1 HETATM 18 N N9 ADP . . . F 3 182.783 282.951 276.545 1 177.95 ? N9 ADP 1601 E 1 HETATM 19 C C8 ADP . . . F 3 182.978 284.276 276.465 1 177.95 ? C8 ADP 1601 E 1 HETATM 20 N N7 ADP . . . F 3 183.039 284.684 275.176 1 177.95 ? N7 ADP 1601 E 1 HETATM 21 C C5 ADP . . . F 3 182.89 283.595 274.411 1 177.95 ? C5 ADP 1601 E 1 HETATM 22 C C6 ADP . . . F 3 182.843 283.299 272.964 1 177.95 ? C6 ADP 1601 E 1 HETATM 23 N N6 ADP . . . F 3 182.987 284.282 272.046 1 177.95 ? N6 ADP 1601 E 1 HETATM 24 N N1 ADP . . . F 3 182.659 282.016 272.581 1 177.95 ? N1 ADP 1601 E 1 HETATM 25 C C2 ADP . . . F 3 182.514 281.016 273.47 1 177.95 ? C2 ADP 1601 E 1 HETATM 26 N N3 ADP . . . F 3 182.541 281.218 274.798 1 177.95 ? N3 ADP 1601 E 1 HETATM 27 C C4 ADP . . . F 3 182.726 282.453 275.315 1 177.95 ? C4 ADP 1601 E 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #