data_8KG2 # _model_server_result.job_id 1vmzjIsMq82vbcQluHsjuQ _model_server_result.datetime_utc '2024-12-05 03:29:34' _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 8kg2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":501}' # _entry.id 8KG2 # _exptl.entry_id 8KG2 _exptl.method 'X-RAY DIFFRACTION' # _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 71.52 _cell.angle_beta 80.87 _cell.angle_gamma 87.53 _cell.entry_id 8KG2 _cell.length_a 106.665 _cell.length_b 134.484 _cell.length_c 148.223 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KG2 _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 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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 _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 ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 CA N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N ? 3 HA N N ? 3 IA N N ? 3 JA N N # _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 8KG2 _atom_sites.fract_transf_matrix[1][1] 0.009375 _atom_sites.fract_transf_matrix[1][2] -0.000404 _atom_sites.fract_transf_matrix[1][3] -0.001453 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007443 _atom_sites.fract_transf_matrix[2][3] -0.002465 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007198 _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 Y 3 ADP A 1 501 501 ADP ADP . Z 3 ADP B 1 501 501 ADP ADP . AA 3 ADP C 1 501 501 ADP ADP . BA 3 ADP D 1 501 501 ADP ADP . CA 3 ADP E 1 501 501 ADP ADP . DA 3 ADP F 1 501 501 ADP ADP . EA 3 ADP G 1 501 501 ADP ADP . FA 3 ADP H 1 501 501 ADP ADP . GA 3 ADP I 1 501 501 ADP ADP . HA 3 ADP J 1 501 501 ADP ADP . IA 3 ADP K 1 501 501 ADP ADP . JA 3 ADP L 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 . . . AA 3 23.242 3.357 -9.845 1 66.52 ? PB ADP 501 C 1 HETATM 2 O O1B ADP . . . AA 3 24.386 2.513 -10.375 1 68.52 ? O1B ADP 501 C 1 HETATM 3 O O2B ADP . . . AA 3 21.959 2.562 -9.631 1 64.8 ? O2B ADP 501 C 1 HETATM 4 O O3B ADP . . . AA 3 23.634 4.194 -8.64 1 67.47 ? O3B ADP 501 C 1 HETATM 5 P PA ADP . . . AA 3 23.789 5.468 -11.801 1 64.98 ? PA ADP 501 C 1 HETATM 6 O O1A ADP . . . AA 3 25.205 5.012 -11.741 1 83.25 ? O1A ADP 501 C 1 HETATM 7 O O2A ADP . . . AA 3 23.488 6.844 -11.305 1 62.23 ? O2A ADP 501 C 1 HETATM 8 O O3A ADP . . . AA 3 22.894 4.414 -11.004 1 66.96 ? O3A ADP 501 C 1 HETATM 9 O O5' ADP . . . AA 3 23.248 5.24 -13.294 1 60.49 ? O5' ADP 501 C 1 HETATM 10 C C5' ADP . . . AA 3 24.27 5.196 -14.32 1 55.93 ? C5' ADP 501 C 1 HETATM 11 C C4' ADP . . . AA 3 23.834 6.095 -15.441 1 56.21 ? C4' ADP 501 C 1 HETATM 12 O O4' ADP . . . AA 3 22.539 5.627 -15.865 1 56.83 ? O4' ADP 501 C 1 HETATM 13 C C3' ADP . . . AA 3 23.581 7.557 -15.074 1 66.6 ? C3' ADP 501 C 1 HETATM 14 O O3' ADP . . . AA 3 24.74 8.322 -15.364 1 94.6 ? O3' ADP 501 C 1 HETATM 15 C C2' ADP . . . AA 3 22.556 7.981 -16.118 1 65.96 ? C2' ADP 501 C 1 HETATM 16 O O2' ADP . . . AA 3 23.243 8.283 -17.315 1 77.16 ? O2' ADP 501 C 1 HETATM 17 C C1' ADP . . . AA 3 21.738 6.704 -16.275 1 60.41 ? C1' ADP 501 C 1 HETATM 18 N N9 ADP . . . AA 3 20.516 6.65 -15.494 1 55.48 ? N9 ADP 501 C 1 HETATM 19 C C8 ADP . . . AA 3 20.203 5.714 -14.542 1 60.41 ? C8 ADP 501 C 1 HETATM 20 N N7 ADP . . . AA 3 19.014 5.883 -14.015 1 60.41 ? N7 ADP 501 C 1 HETATM 21 C C5 ADP . . . AA 3 18.509 7 -14.664 1 51.83 ? C5 ADP 501 C 1 HETATM 22 C C6 ADP . . . AA 3 17.286 7.687 -14.547 1 47.05 ? C6 ADP 501 C 1 HETATM 23 N N6 ADP . . . AA 3 16.326 7.348 -13.698 1 45.95 ? N6 ADP 501 C 1 HETATM 24 N N1 ADP . . . AA 3 17.086 8.749 -15.36 1 51.97 ? N1 ADP 501 C 1 HETATM 25 C C2 ADP . . . AA 3 18.066 9.084 -16.213 1 59.73 ? C2 ADP 501 C 1 HETATM 26 N N3 ADP . . . AA 3 19.266 8.531 -16.396 1 51.67 ? N3 ADP 501 C 1 HETATM 27 C C4 ADP . . . AA 3 19.425 7.475 -15.587 1 52.37 ? C4 ADP 501 C 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 154 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #