data_9E8O # _model_server_result.job_id RQDnPXn7m4YGGoV6RezOeQ _model_server_result.datetime_utc '2024-12-20 14:20:08' _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 9e8o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"QA","auth_seq_id":501}' # _entry.id 9E8O # _exptl.entry_id 9E8O _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 37 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 9E8O _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9E8O _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 34-meric _pdbx_struct_assembly.oligomeric_count 34 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 37 MA N N ? 37 PA N N ? 37 QA N N ? 37 RA N 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 DA SG CYS 396 F CYS 396 1_555 DA SG CYS 400 F CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 FA SG CYS 633 U CYS 633 1_555 FA SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 GA C PHE 226 g PHE 226 1_555 GA N1 CR8 227 g CR8 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 GA C3 CR8 227 g CR8 228 1_555 GA N ASN 228 g ASN 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? metalc ? metalc1 A OG1 THR 233 B THR 233 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc2 IA O1G ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc3 IA O2G ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc4 IA O1B ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc5 IA O3B ATP . B ATP 501 1_555 JA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc6 B OG1 THR 197 C THR 197 1_555 LA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc7 KA O1G ATP . C ATP 501 1_555 LA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc8 KA O2G ATP . C ATP 501 1_555 LA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc9 C OG1 THR 213 D THR 213 1_555 NA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc10 MA O2B ADP . D ADP 501 1_555 NA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc11 D NE2 HIS 113 c HIS 113 1_555 OA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc12 D NE2 HIS 115 c HIS 115 1_555 OA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc13 D OD1 ASP 126 c ASP 126 1_555 OA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc14 D OD2 ASP 126 c ASP 126 1_555 OA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? # _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 9E8O _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 IA 35 ATP B 1 501 501 ATP ATP . JA 36 MG B 1 502 502 MG MG . KA 35 ATP C 1 501 501 ATP ATP . LA 36 MG C 1 502 502 MG MG . MA 37 ADP D 1 501 501 ADP ADP . NA 36 MG D 1 502 502 MG MG . OA 38 ZN c 1 501 401 ZN ZN . PA 37 ADP A 1 501 501 ADP ADP . QA 37 ADP F 1 501 501 ADP ADP . RA 37 ADP E 1 501 501 ADP ADP . # 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 . . . QA 37 218.135 161.744 165.883 1 273.18 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . QA 37 217.326 160.88 164.951 1 267.31 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . QA 37 218.349 163.16 165.402 1 265.29 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . QA 37 217.737 161.631 167.334 1 274.83 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . QA 37 220.57 161.226 164.566 1 260.21 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . QA 37 220.025 160.404 163.425 1 257.37 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . QA 37 220.888 162.688 164.382 1 253.95 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . QA 37 219.6 161.083 165.842 1 265.44 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . QA 37 221.887 160.503 165.132 1 257.56 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . QA 37 223.078 161.258 165.311 1 256.63 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . QA 37 224.218 160.313 165.648 1 258.92 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . QA 37 224.415 159.382 164.58 1 259.93 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . QA 37 225.514 161.083 165.828 1 257.04 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . QA 37 226.089 160.745 167.091 1 259.62 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . QA 37 226.406 160.61 164.7 1 255.51 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . QA 37 227.76 160.428 165.103 1 253.91 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . QA 37 225.811 159.286 164.282 1 258.65 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . QA 37 226.04 158.931 162.858 1 257.14 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . QA 37 225.279 158.058 162.186 1 257.35 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . QA 37 225.704 157.879 160.916 1 256 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . QA 37 226.784 158.657 160.759 1 254.74 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . QA 37 227.717 158.938 159.651 1 252.87 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . QA 37 227.567 158.345 158.443 1 251.1 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . QA 37 228.713 159.815 159.883 1 251.97 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . QA 37 228.868 160.41 161.079 1 250.98 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . QA 37 228.063 160.195 162.129 1 251 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . QA 37 227.016 159.341 162.041 1 254.58 ? C4 ADP 501 F 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 434 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #