data_6TDY # _model_server_result.job_id RG0Qx1OkbocSNvx5li_iNw _model_server_result.datetime_utc '2024-12-26 10:23:18' _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 6tdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":601}' # _entry.id 6TDY # _exptl.entry_id 6TDY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 14 _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 6TDY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TDY _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 26-meric _pdbx_struct_assembly.oligomeric_count 26 _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 _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 14 _struct_asym.id GA _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 190 A THR 191 1_555 BA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc2 AA O3G ATP . A ATP 601 1_555 BA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc3 AA O2B ATP . A ATP 601 1_555 BA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc4 B OG1 THR 190 B THR 191 1_555 DA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 CA O3G ATP . B ATP 601 1_555 DA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc6 CA O2B ATP . B ATP 601 1_555 DA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc7 C OG1 THR 190 C THR 191 1_555 FA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc8 EA O1G ATP . C ATP 601 1_555 FA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc9 EA O2B ATP . C ATP 601 1_555 FA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc10 D OG1 THR 167 D THR 174 1_555 HA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc11 GA O3B ADP . D ADP 601 1_555 HA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc12 F OG1 THR 167 F THR 174 1_555 KA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc13 JA O3G ATP . F ATP 601 1_555 KA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc14 JA O2B ATP . F ATP 601 1_555 KA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? # _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 6TDY _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 AA 12 ATP A 1 601 2 ATP ATP . BA 13 MG A 1 602 1 MG MG . CA 12 ATP B 1 601 3 ATP ATP . DA 13 MG B 1 602 2 MG MG . EA 12 ATP C 1 601 1 ATP ATP . FA 13 MG C 1 602 5 MG MG . GA 14 ADP D 1 601 5 ADP ADP . HA 13 MG D 1 602 4 MG MG . IA 15 TRT E 1 600 600 TRT TRT . JA 12 ATP F 1 601 4 ATP ATP . KA 13 MG F 1 602 3 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 . . . GA 14 308.915 221.339 313.625 1 36.03 ? PB ADP 601 D 1 HETATM 2 O O1B ADP . . . GA 14 309.927 220.642 312.766 1 36.03 ? O1B ADP 601 D 1 HETATM 3 O O2B ADP . . . GA 14 307.768 220.478 314.066 1 36.03 ? O2B ADP 601 D 1 HETATM 4 O O3B ADP . . . GA 14 309.492 222.206 314.711 1 36.03 ? O3B ADP 601 D 1 HETATM 5 P PA ADP . . . GA 14 306.915 223.182 313.063 1 36.03 ? PA ADP 601 D 1 HETATM 6 O O1A ADP . . . GA 14 305.844 222.22 313.49 1 36.03 ? O1A ADP 601 D 1 HETATM 7 O O2A ADP . . . GA 14 307.391 224.28 313.972 1 36.03 ? O2A ADP 601 D 1 HETATM 8 O O3A ADP . . . GA 14 308.204 222.347 312.616 1 36.03 ? O3A ADP 601 D 1 HETATM 9 O O5' ADP . . . GA 14 306.453 223.828 311.679 1 36.03 ? O5' ADP 601 D 1 HETATM 10 C C5' ADP . . . GA 14 307.441 224.535 310.977 1 36.03 ? C5' ADP 601 D 1 HETATM 11 C C4' ADP . . . GA 14 306.974 225.193 309.695 1 36.03 ? C4' ADP 601 D 1 HETATM 12 O O4' ADP . . . GA 14 306.472 224.259 308.74 1 36.03 ? O4' ADP 601 D 1 HETATM 13 C C3' ADP . . . GA 14 305.857 226.152 309.965 1 36.03 ? C3' ADP 601 D 1 HETATM 14 O O3' ADP . . . GA 14 306.4 227.373 310.43 1 36.03 ? O3' ADP 601 D 1 HETATM 15 C C2' ADP . . . GA 14 305.189 226.226 308.616 1 36.03 ? C2' ADP 601 D 1 HETATM 16 O O2' ADP . . . GA 14 305.85 227.174 307.783 1 36.03 ? O2' ADP 601 D 1 HETATM 17 C C1' ADP . . . GA 14 305.369 224.838 308.041 1 36.03 ? C1' ADP 601 D 1 HETATM 18 N N9 ADP . . . GA 14 304.156 224.024 308.275 1 36.03 ? N9 ADP 601 D 1 HETATM 19 C C8 ADP . . . GA 14 304.055 223.019 309.156 1 36.03 ? C8 ADP 601 D 1 HETATM 20 N N7 ADP . . . GA 14 302.815 222.476 309.132 1 36.03 ? N7 ADP 601 D 1 HETATM 21 C C5 ADP . . . GA 14 302.103 223.147 308.215 1 36.03 ? C5 ADP 601 D 1 HETATM 22 C C6 ADP . . . GA 14 300.73 223.086 307.688 1 36.03 ? C6 ADP 601 D 1 HETATM 23 N N6 ADP . . . GA 14 299.857 222.175 308.159 1 36.03 ? N6 ADP 601 D 1 HETATM 24 N N1 ADP . . . GA 14 300.387 223.968 306.732 1 36.03 ? N1 ADP 601 D 1 HETATM 25 C C2 ADP . . . GA 14 301.256 224.876 306.263 1 36.03 ? C2 ADP 601 D 1 HETATM 26 N N3 ADP . . . GA 14 302.518 224.986 306.697 1 36.03 ? N3 ADP 601 D 1 HETATM 27 C C4 ADP . . . GA 14 302.993 224.16 307.649 1 36.03 ? C4 ADP 601 D 1 HETATM 28 H "H5'1" ADP . . . GA 14 308.214 223.849 310.745 1 36.03 ? "H5'1" ADP 601 D 1 HETATM 29 H "H5'2" ADP . . . GA 14 307.858 225.281 311.641 1 36.03 ? "H5'2" ADP 601 D 1 HETATM 30 H H4' ADP . . . GA 14 307.81 225.746 309.263 1 36.03 ? H4' ADP 601 D 1 HETATM 31 H H3' ADP . . . GA 14 305.155 225.722 310.689 1 36.03 ? H3' ADP 601 D 1 HETATM 32 H HO3' ADP . . . GA 14 305.898 227.586 311.217 1 36.03 ? HO3' ADP 601 D 1 HETATM 33 H H2' ADP . . . GA 14 304.128 226.471 308.728 1 36.03 ? H2' ADP 601 D 1 HETATM 34 H HO2' ADP . . . GA 14 305.754 228.055 308.16 1 36.03 ? HO2' ADP 601 D 1 HETATM 35 H H1' ADP . . . GA 14 305.582 224.912 306.976 1 36.03 ? H1' ADP 601 D 1 HETATM 36 H H8 ADP . . . GA 14 304.854 222.687 309.8 1 36.03 ? H8 ADP 601 D 1 HETATM 37 H HN61 ADP . . . GA 14 300.147 221.529 308.878 1 36.03 ? HN61 ADP 601 D 1 HETATM 38 H HN62 ADP . . . GA 14 298.918 222.142 307.791 1 36.03 ? HN62 ADP 601 D 1 HETATM 39 H H2 ADP . . . GA 14 300.923 225.556 305.496 1 36.03 ? H2 ADP 601 D 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 92 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 39 #