data_9RAI # _model_server_result.job_id eVCJUiY3pui2BHAeOuYgNw _model_server_result.datetime_utc '2025-09-30 23:55:52' _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 9rai # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":902}' # _entry.id 9RAI # _exptl.entry_id 9RAI _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 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 9RAI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9RAI _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 27-meric _pdbx_struct_assembly.oligomeric_count 27 _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,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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 BA N N ? 5 DA N N ? 5 NA N N ? 5 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 metalc ? metalc1 I OG1 THR 215 b THR 215 1_555 EA MG MG . b MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc2 I OD2 ASP 279 b ASP 279 1_555 EA MG MG . b MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc3 I OD1 ASP 635 b ASP 635 1_555 IA MG MG . c MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 I OD2 ASP 635 b ASP 635 1_555 IA MG MG . c MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc5 CA O2G AGS . b AGS 901 1_555 EA MG MG . b MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc6 CA O2B AGS . b AGS 901 1_555 EA MG MG . b MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc7 J OG1 THR 215 c THR 215 1_555 HA MG MG . c MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc8 J OD1 ASP 279 c ASP 279 1_555 HA MG MG . c MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc9 J OD2 ASP 279 c ASP 279 1_555 HA MG MG . c MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc10 J NE ARG 763 c ARG 763 1_555 IA MG MG . c MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc11 J NH2 ARG 763 c ARG 763 1_555 IA MG MG . c MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc12 K OG1 THR 215 d THR 215 1_555 LA MG MG . d MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc13 K OD1 ASP 279 d ASP 279 1_555 LA MG MG . d MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc14 K OD2 ASP 279 d ASP 279 1_555 LA MG MG . d MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc15 K OG1 THR 552 d THR 552 1_555 MA MG MG . d MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc16 KA O2G AGS . d AGS 901 1_555 MA MG MG . d MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc17 KA O2B AGS . d AGS 901 1_555 MA MG MG . d MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc18 L OG1 THR 215 e THR 215 1_555 QA MG MG . e MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc19 L OD2 ASP 279 e ASP 279 1_555 QA MG MG . e MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc20 L OG1 THR 552 e THR 552 1_555 PA MG MG . e MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc21 L OD1 ASP 617 e ASP 617 1_555 PA MG MG . e MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc22 NA O2B ADP . e ADP 901 1_555 QA MG MG . e MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc23 OA O2G AGS . e AGS 902 1_555 PA MG MG . e MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc24 OA O3G AGS . e AGS 902 1_555 PA MG MG . e MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? # _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 9RAI _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 BA 5 ADP a 1 901 901 ADP ADP ? CA 6 AGS b 1 901 901 AGS AGS ? DA 5 ADP b 1 902 902 ADP ADP ? EA 7 MG b 1 903 903 MG MG ? FA 6 AGS c 1 901 901 AGS AGS ? GA 6 AGS c 1 902 902 AGS AGS ? HA 7 MG c 1 903 903 MG MG ? IA 7 MG c 1 904 904 MG MG ? JA 6 AGS c 1 905 901 AGS AGS ? KA 6 AGS d 1 901 902 AGS AGS ? LA 7 MG d 1 902 903 MG MG ? MA 7 MG d 1 903 904 MG MG ? NA 5 ADP e 1 901 901 ADP ADP ? OA 6 AGS e 1 902 902 AGS AGS ? PA 7 MG e 1 903 903 MG MG ? QA 7 MG e 1 904 904 MG MG ? RA 5 ADP f 1 901 902 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 . . . DA 5 210.544 165.443 206.23 1 90.06 ? PB ADP 902 b 1 HETATM 2 O O1B ADP . . . DA 5 209.847 164.197 206.718 1 62.02 ? O1B ADP 902 b 1 HETATM 3 O O2B ADP . . . DA 5 210.046 165.964 204.903 1 77.34 ? O2B ADP 902 b 1 HETATM 4 O O3B ADP . . . DA 5 210.708 166.51 207.286 1 63.87 ? O3B ADP 902 b 1 HETATM 5 P PA ADP . . . DA 5 212.342 163.744 204.894 1 90.62 ? PA ADP 902 b 1 HETATM 6 O O1A ADP . . . DA 5 211.532 162.544 205.316 1 60.44 ? O1A ADP 902 b 1 HETATM 7 O O2A ADP . . . DA 5 212.218 164.249 203.479 1 87.18 ? O2A ADP 902 b 1 HETATM 8 O O3A ADP . . . DA 5 212.047 164.946 205.927 1 96.8 ? O3A ADP 902 b 1 HETATM 9 O O5' ADP . . . DA 5 213.886 163.385 205.163 1 76.35 ? O5' ADP 902 b 1 HETATM 10 C C5' ADP . . . DA 5 214.189 162.176 205.849 1 69.65 ? C5' ADP 902 b 1 HETATM 11 C C4' ADP . . . DA 5 215.476 161.546 205.345 1 60.22 ? C4' ADP 902 b 1 HETATM 12 O O4' ADP . . . DA 5 215.767 160.435 206.192 1 65.19 ? O4' ADP 902 b 1 HETATM 13 C C3' ADP . . . DA 5 215.308 161.02 203.932 1 58.76 ? C3' ADP 902 b 1 HETATM 14 O O3' ADP . . . DA 5 216.372 161.491 203.103 1 53.55 ? O3' ADP 902 b 1 HETATM 15 C C2' ADP . . . DA 5 215.379 159.512 204.035 1 61.52 ? C2' ADP 902 b 1 HETATM 16 O O2' ADP . . . DA 5 216.393 159.021 203.155 1 58.49 ? O2' ADP 902 b 1 HETATM 17 C C1' ADP . . . DA 5 215.751 159.201 205.473 1 61.62 ? C1' ADP 902 b 1 HETATM 18 N N9 ADP . . . DA 5 214.747 158.296 206.088 1 60.4 ? N9 ADP 902 b 1 HETATM 19 C C8 ADP . . . DA 5 213.924 158.601 207.106 1 61.01 ? C8 ADP 902 b 1 HETATM 20 N N7 ADP . . . DA 5 213.137 157.543 207.436 1 65.4 ? N7 ADP 902 b 1 HETATM 21 C C5 ADP . . . DA 5 213.452 156.524 206.618 1 61.96 ? C5 ADP 902 b 1 HETATM 22 C C6 ADP . . . DA 5 213.008 155.119 206.421 1 62.73 ? C6 ADP 902 b 1 HETATM 23 N N6 ADP . . . DA 5 212.032 154.517 207.167 1 68.09 ? N6 ADP 902 b 1 HETATM 24 N N1 ADP . . . DA 5 213.629 154.432 205.44 1 65.65 ? N1 ADP 902 b 1 HETATM 25 C C2 ADP . . . DA 5 214.597 154.956 204.671 1 61.68 ? C2 ADP 902 b 1 HETATM 26 N N3 ADP . . . DA 5 215.041 156.212 204.797 1 60.52 ? N3 ADP 902 b 1 HETATM 27 C C4 ADP . . . DA 5 214.52 157.03 205.736 1 62.16 ? C4 ADP 902 b 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #