data_1YT0 # _model_server_result.job_id T9fEPp514BdxqG2FsQchZQ _model_server_result.datetime_utc '2024-10-12 23:26:10' _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 1yt0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":339}' # _entry.id 1YT0 # _exptl.entry_id 1YT0 _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 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 1YT0 _cell.length_a 65.91 _cell.length_b 94.86 _cell.length_c 42.91 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YT0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 J O HOH . A HOH 4 1_555 B MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc2 J O HOH . A HOH 5 1_555 B MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc3 A OD1 ASN 43 A ASN 107 1_555 B MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc4 B MG MG . A MG 338 1_555 C O1B ADP . A ADP 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc5 B MG MG . A MG 338 1_555 C O2A ADP . A ADP 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? # _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 1YT0 _atom_sites.fract_transf_matrix[1][1] 0.015172 _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] 0.010542 _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] 0.023305 _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 B 2 MG A 1 338 1 MG MG . C 3 ADP A 1 339 1 ADP ADP . D 4 PG4 A 1 301 1 PG4 PG4 . E 4 PG4 A 1 302 2 PG4 PG4 . F 4 PG4 A 1 306 6 PG4 PG4 . G 4 PG4 A 1 307 7 PG4 PG4 . H 4 PG4 A 1 308 8 PG4 PG4 . I 4 PG4 A 1 309 9 PG4 PG4 . J 5 HOH A 1 1 1 HOH HOH . J 5 HOH A 2 2 2 HOH HOH . J 5 HOH A 3 3 3 HOH HOH . J 5 HOH A 4 4 4 HOH HOH . J 5 HOH A 5 5 5 HOH HOH . J 5 HOH A 6 6 6 HOH HOH . J 5 HOH A 7 7 7 HOH HOH . J 5 HOH A 8 8 8 HOH HOH . J 5 HOH A 9 9 9 HOH HOH . J 5 HOH A 10 10 10 HOH HOH . J 5 HOH A 11 11 11 HOH HOH . J 5 HOH A 12 12 12 HOH HOH . J 5 HOH A 13 13 13 HOH HOH . J 5 HOH A 14 14 14 HOH HOH . J 5 HOH A 15 15 15 HOH HOH . J 5 HOH A 16 16 16 HOH HOH . J 5 HOH A 17 17 17 HOH HOH . J 5 HOH A 18 18 18 HOH HOH . J 5 HOH A 19 19 19 HOH HOH . J 5 HOH A 20 20 20 HOH HOH . J 5 HOH A 21 21 21 HOH HOH . J 5 HOH A 22 22 22 HOH HOH . J 5 HOH A 23 23 23 HOH HOH . J 5 HOH A 24 24 24 HOH HOH . J 5 HOH A 25 25 25 HOH HOH . J 5 HOH A 26 26 26 HOH HOH . J 5 HOH A 27 27 27 HOH HOH . J 5 HOH A 28 28 28 HOH HOH . J 5 HOH A 29 29 29 HOH HOH . J 5 HOH A 30 30 30 HOH HOH . J 5 HOH A 31 31 31 HOH HOH . J 5 HOH A 32 32 32 HOH HOH . J 5 HOH A 33 33 33 HOH HOH . J 5 HOH A 34 34 34 HOH HOH . J 5 HOH A 35 35 35 HOH HOH . J 5 HOH A 36 36 36 HOH HOH . J 5 HOH A 37 37 37 HOH HOH . J 5 HOH A 38 38 38 HOH HOH . J 5 HOH A 39 39 39 HOH HOH . J 5 HOH A 40 40 40 HOH HOH . J 5 HOH A 41 41 41 HOH HOH . J 5 HOH A 42 42 42 HOH HOH . J 5 HOH A 43 43 43 HOH HOH . J 5 HOH A 44 44 44 HOH HOH . J 5 HOH A 45 45 45 HOH HOH . J 5 HOH A 46 46 46 HOH HOH . J 5 HOH A 47 47 47 HOH HOH . J 5 HOH A 48 48 48 HOH HOH . J 5 HOH A 49 49 49 HOH HOH . J 5 HOH A 50 50 50 HOH HOH . J 5 HOH A 51 51 51 HOH HOH . J 5 HOH A 52 52 52 HOH HOH . J 5 HOH A 53 53 53 HOH HOH . J 5 HOH A 54 54 54 HOH HOH . J 5 HOH A 55 55 55 HOH HOH . J 5 HOH A 56 56 56 HOH HOH . J 5 HOH A 57 57 57 HOH HOH . J 5 HOH A 58 58 58 HOH HOH . J 5 HOH A 59 59 59 HOH HOH . J 5 HOH A 60 60 60 HOH HOH . J 5 HOH A 61 61 61 HOH HOH . J 5 HOH A 62 62 62 HOH HOH . J 5 HOH A 63 63 63 HOH HOH . J 5 HOH A 64 64 64 HOH HOH . # 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 . . . C 3 16.596 34.865 15.005 1 51.93 ? PB ADP 339 A 1 HETATM 2 O O1B ADP . . . C 3 16.451 33.423 14.7 1 52.54 ? O1B ADP 339 A 1 HETATM 3 O O2B ADP . . . C 3 16.993 35.13 16.543 1 50.05 ? O2B ADP 339 A 1 HETATM 4 O O3B ADP . . . C 3 17.739 35.576 14.122 1 53.41 ? O3B ADP 339 A 1 HETATM 5 P PA ADP . . . C 3 13.836 35.077 14.403 1 51.28 ? PA ADP 339 A 1 HETATM 6 O O1A ADP . . . C 3 12.914 36.19 14.084 1 52 ? O1A ADP 339 A 1 HETATM 7 O O2A ADP . . . C 3 14.03 34.008 13.397 1 50.09 ? O2A ADP 339 A 1 HETATM 8 O O3A ADP . . . C 3 15.263 35.737 14.751 1 50.87 ? O3A ADP 339 A 1 HETATM 9 O O5' ADP . . . C 3 13.373 34.403 15.79 1 52.46 ? O5' ADP 339 A 1 HETATM 10 C C5' ADP . . . C 3 13.408 35.124 17.025 1 52.11 ? C5' ADP 339 A 1 HETATM 11 C C4' ADP . . . C 3 13.389 34.132 18.189 1 54.12 ? C4' ADP 339 A 1 HETATM 12 O O4' ADP . . . C 3 12.21 33.31 18.21 1 54.23 ? O4' ADP 339 A 1 HETATM 13 C C3' ADP . . . C 3 14.514 33.115 17.996 1 54.52 ? C3' ADP 339 A 1 HETATM 14 O O3' ADP . . . C 3 15.755 33.718 18.371 1 57.11 ? O3' ADP 339 A 1 HETATM 15 C C2' ADP . . . C 3 14.08 32.108 19.058 1 52.79 ? C2' ADP 339 A 1 HETATM 16 O O2' ADP . . . C 3 14.367 32.626 20.36 1 52.14 ? O2' ADP 339 A 1 HETATM 17 C C1' ADP . . . C 3 12.565 32.061 18.834 1 51.76 ? C1' ADP 339 A 1 HETATM 18 N N9 ADP . . . C 3 12.175 30.963 17.919 1 50.48 ? N9 ADP 339 A 1 HETATM 19 C C8 ADP . . . C 3 11.702 31.108 16.681 1 51.55 ? C8 ADP 339 A 1 HETATM 20 N N7 ADP . . . C 3 11.41 29.918 16.167 1 47.82 ? N7 ADP 339 A 1 HETATM 21 C C5 ADP . . . C 3 11.7 28.997 17.085 1 46.15 ? C5 ADP 339 A 1 HETATM 22 C C6 ADP . . . C 3 11.598 27.611 17.113 1 42.8 ? C6 ADP 339 A 1 HETATM 23 N N6 ADP . . . C 3 11.173 26.937 16.047 1 30.6 ? N6 ADP 339 A 1 HETATM 24 N N1 ADP . . . C 3 11.993 26.934 18.275 1 41.86 ? N1 ADP 339 A 1 HETATM 25 C C2 ADP . . . C 3 12.484 27.664 19.366 1 44.5 ? C2 ADP 339 A 1 HETATM 26 N N3 ADP . . . C 3 12.569 28.981 19.295 1 49.27 ? N3 ADP 339 A 1 HETATM 27 C C4 ADP . . . C 3 12.191 29.663 18.199 1 48.19 ? C4 ADP 339 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #