data_8Y1T # _model_server_result.job_id go9yMw7ESTHMpFq3ea6QwQ _model_server_result.datetime_utc '2025-07-14 12:24:47' _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 8y1t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":603}' # _entry.id 8Y1T # _exptl.entry_id 8Y1T _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 2 _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 8Y1T _cell.length_a 62.563 _cell.length_b 121.741 _cell.length_c 154.278 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y1T _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D N N ? 3 H 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 8Y1T _atom_sites.fract_transf_matrix[1][1] 0.015984 _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] 0.008214 _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] 0.006482 _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 C 2 G3P A 1 601 601 G3P G3P . D 3 ADP A 1 602 701 ADP ADP . E 4 MG A 1 603 801 MG MG . F 5 GOL B 1 601 601 GOL GOL . G 5 GOL B 1 602 602 GOL GOL . H 3 ADP B 1 603 701 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 . . . H 3 -50.833 31.187 -34.303 1 107.69 ? PB ADP 603 B 1 HETATM 2 O O1B ADP . . . H 3 -51.019 31.147 -35.772 1 118.59 ? O1B ADP 603 B 1 HETATM 3 O O2B ADP . . . H 3 -52.106 31.267 -33.548 1 112.45 ? O2B ADP 603 B 1 HETATM 4 O O3B ADP . . . H 3 -49.846 32.198 -33.841 1 116.45 ? O3B ADP 603 B 1 HETATM 5 P PA ADP . . . H 3 -49.194 28.95 -34.731 1 79.34 ? PA ADP 603 B 1 HETATM 6 O O1A ADP . . . H 3 -49.327 29.285 -36.157 1 75.84 ? O1A ADP 603 B 1 HETATM 7 O O2A ADP . . . H 3 -47.884 29.022 -34.055 1 82.58 ? O2A ADP 603 B 1 HETATM 8 O O3A ADP . . . H 3 -50.216 29.78 -33.875 1 95.28 ? O3A ADP 603 B 1 HETATM 9 O O5' ADP . . . H 3 -49.731 27.487 -34.546 1 79.09 ? O5' ADP 603 B 1 HETATM 10 C C5' ADP . . . H 3 -49.499 26.769 -33.35 1 74.75 ? C5' ADP 603 B 1 HETATM 11 C C4' ADP . . . H 3 -50.434 25.575 -33.257 1 69.81 ? C4' ADP 603 B 1 HETATM 12 O O4' ADP . . . H 3 -51.78 25.994 -33.338 1 67.14 ? O4' ADP 603 B 1 HETATM 13 C C3' ADP . . . H 3 -50.253 24.68 -34.435 1 65.28 ? C3' ADP 603 B 1 HETATM 14 O O3' ADP . . . H 3 -50.636 23.403 -34.024 1 67.93 ? O3' ADP 603 B 1 HETATM 15 C C2' ADP . . . H 3 -51.318 25.087 -35.383 1 67.13 ? C2' ADP 603 B 1 HETATM 16 O O2' ADP . . . H 3 -51.669 23.962 -36.15 1 61.7 ? O2' ADP 603 B 1 HETATM 17 C C1' ADP . . . H 3 -52.43 25.416 -34.447 1 65.16 ? C1' ADP 603 B 1 HETATM 18 N N9 ADP . . . H 3 -53.337 26.372 -35.091 1 63.05 ? N9 ADP 603 B 1 HETATM 19 C C8 ADP . . . H 3 -53.107 27.655 -35.294 1 63.15 ? C8 ADP 603 B 1 HETATM 20 N N7 ADP . . . H 3 -54.147 28.235 -35.905 1 66.42 ? N7 ADP 603 B 1 HETATM 21 C C5 ADP . . . H 3 -55.069 27.306 -36.111 1 63.07 ? C5 ADP 603 B 1 HETATM 22 C C6 ADP . . . H 3 -56.411 27.24 -36.711 1 67.2 ? C6 ADP 603 B 1 HETATM 23 N N6 ADP . . . H 3 -57.008 28.312 -37.241 1 61.87 ? N6 ADP 603 B 1 HETATM 24 N N1 ADP . . . H 3 -57.041 26.069 -36.713 1 64.9 ? N1 ADP 603 B 1 HETATM 25 C C2 ADP . . . H 3 -56.471 24.989 -36.189 1 72.21 ? C2 ADP 603 B 1 HETATM 26 N N3 ADP . . . H 3 -55.265 24.976 -35.633 1 65.88 ? N3 ADP 603 B 1 HETATM 27 C C4 ADP . . . H 3 -54.526 26.084 -35.565 1 61.83 ? C4 ADP 603 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #