data_7NFY # _model_server_result.job_id DWxkPrecZDgF3LJqvEWMEw _model_server_result.datetime_utc '2024-11-21 17:08:29' _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 7nfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1001}' # _entry.id 7NFY # _exptl.entry_id 7NFY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 7NFY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NFY _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 PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,H,I,J,K,L,M,N,O,P,Q,R _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 5 _struct_asym.id P _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 424 A THR 530 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc3 H O1B AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 B OG1 THR 424 B THR 530 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc5 J O2G AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc6 J O1B AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc7 C OG1 THR 424 C THR 530 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 L O2G AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc9 L O1B AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc10 D OG1 THR 424 D THR 530 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc11 N O2G AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 N O1B AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc13 F OG1 THR 424 F THR 530 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc14 Q O2G AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc15 Q O1B AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? # _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 7NFY _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 H 3 AGS A 1 1001 1001 AGS AGS . I 4 MG A 1 1002 1002 MG MG . J 3 AGS B 1 1001 1001 AGS AGS . K 4 MG B 1 1002 1002 MG MG . L 3 AGS C 1 1001 1001 AGS AGS . M 4 MG C 1 1002 1002 MG MG . N 3 AGS D 1 1001 1001 AGS AGS . O 4 MG D 1 1002 1002 MG MG . P 5 ADP E 1 1001 1001 ADP ADP . Q 3 AGS F 1 1001 1001 AGS AGS . R 4 MG F 1 1002 1002 MG MG . # 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 . . . P 5 183.726 194.449 238.367 1 110.94 ? PB ADP 1001 E 1 HETATM 2 O O1B ADP . . . P 5 183.411 195.78 237.752 1 110.94 ? O1B ADP 1001 E 1 HETATM 3 O O2B ADP . . . P 5 182.748 194.042 239.428 1 110.94 ? O2B ADP 1001 E 1 HETATM 4 O O3B ADP . . . P 5 185.177 194.276 238.692 1 110.94 ? O3B ADP 1001 E 1 HETATM 5 P PA ADP . . . P 5 181.998 193.348 236.516 1 110.94 ? PA ADP 1001 E 1 HETATM 6 O O1A ADP . . . P 5 182.269 193.039 235.079 1 110.94 ? O1A ADP 1001 E 1 HETATM 7 O O2A ADP . . . P 5 181.248 194.572 236.948 1 110.94 ? O2A ADP 1001 E 1 HETATM 8 O O3A ADP . . . P 5 183.403 193.333 237.271 1 110.94 ? O3A ADP 1001 E 1 HETATM 9 O O5' ADP . . . P 5 181.273 192.039 237.039 1 110.94 ? O5' ADP 1001 E 1 HETATM 10 C C5' ADP . . . P 5 182.026 191.052 237.694 1 110.94 ? C5' ADP 1001 E 1 HETATM 11 C C4' ADP . . . P 5 181.107 189.856 237.794 1 110.94 ? C4' ADP 1001 E 1 HETATM 12 O O4' ADP . . . P 5 179.995 190.185 238.596 1 110.94 ? O4' ADP 1001 E 1 HETATM 13 C C3' ADP . . . P 5 180.548 189.448 236.457 1 110.94 ? C3' ADP 1001 E 1 HETATM 14 O O3' ADP . . . P 5 180.856 188.071 236.315 1 110.94 ? O3' ADP 1001 E 1 HETATM 15 C C2' ADP . . . P 5 179.055 189.613 236.582 1 110.94 ? C2' ADP 1001 E 1 HETATM 16 O O2' ADP . . . P 5 178.296 188.586 235.953 1 110.94 ? O2' ADP 1001 E 1 HETATM 17 C C1' ADP . . . P 5 178.827 189.592 238.064 1 110.94 ? C1' ADP 1001 E 1 HETATM 18 N N9 ADP . . . P 5 177.653 190.369 238.453 1 110.94 ? N9 ADP 1001 E 1 HETATM 19 C C8 ADP . . . P 5 177.633 191.211 239.479 1 110.94 ? C8 ADP 1001 E 1 HETATM 20 N N7 ADP . . . P 5 176.426 191.761 239.634 1 110.94 ? N7 ADP 1001 E 1 HETATM 21 C C5 ADP . . . P 5 175.657 191.21 238.723 1 110.94 ? C5 ADP 1001 E 1 HETATM 22 C C6 ADP . . . P 5 174.281 191.384 238.346 1 110.94 ? C6 ADP 1001 E 1 HETATM 23 N N6 ADP . . . P 5 173.547 192.234 239.079 1 110.94 ? N6 ADP 1001 E 1 HETATM 24 N N1 ADP . . . P 5 173.821 190.624 237.349 1 110.94 ? N1 ADP 1001 E 1 HETATM 25 C C2 ADP . . . P 5 174.623 189.777 236.685 1 110.94 ? C2 ADP 1001 E 1 HETATM 26 N N3 ADP . . . P 5 175.908 189.597 236.969 1 110.94 ? N3 ADP 1001 E 1 HETATM 27 C C4 ADP . . . P 5 176.45 190.266 237.975 1 110.94 ? C4 ADP 1001 E 1 HETATM 28 H "H5'1" ADP . . . P 5 182.319 191.396 238.688 1 110.94 ? "H5'1" ADP 1001 E 1 HETATM 29 H "H5'2" ADP . . . P 5 182.922 190.804 237.12 1 110.94 ? "H5'2" ADP 1001 E 1 HETATM 30 H H4' ADP . . . P 5 181.656 189.011 238.232 1 110.94 ? H4' ADP 1001 E 1 HETATM 31 H H3' ADP . . . P 5 180.953 190.033 235.619 1 110.94 ? H3' ADP 1001 E 1 HETATM 32 H HO3' ADP . . . P 5 180.614 187.762 235.433 1 110.94 ? HO3' ADP 1001 E 1 HETATM 33 H H2' ADP . . . P 5 178.767 190.599 236.191 1 110.94 ? H2' ADP 1001 E 1 HETATM 34 H HO2' ADP . . . P 5 178.431 188.63 234.997 1 110.94 ? HO2' ADP 1001 E 1 HETATM 35 H H1' ADP . . . P 5 178.735 188.552 238.408 1 110.94 ? H1' ADP 1001 E 1 HETATM 36 H H8 ADP . . . P 5 178.488 191.469 240.087 1 110.94 ? H8 ADP 1001 E 1 HETATM 37 H HN61 ADP . . . P 5 173.975 192.75 239.833 1 110.94 ? HN61 ADP 1001 E 1 HETATM 38 H HN62 ADP . . . P 5 172.584 192.38 238.879 1 110.94 ? HN62 ADP 1001 E 1 HETATM 39 H H2 ADP . . . P 5 174.209 189.203 235.867 1 110.94 ? H2 ADP 1001 E 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 107 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #