data_4TYN # _model_server_result.job_id '_HsI8cFzha8K1ON57GKHDw' _model_server_result.datetime_utc '2024-10-20 00:40:12' _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 4tyn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":603}' # _entry.id 4TYN # _exptl.entry_id 4TYN _exptl.method 'X-RAY DIFFRACTION' # _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 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 4TYN _cell.length_a 90.389 _cell.length_b 126.189 _cell.length_c 55.231 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TYN _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 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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id MG _struct_conn.ptnr1_label_comp_id MG _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id MG _struct_conn.ptnr1_auth_seq_id 601 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id O3B _struct_conn.ptnr2_label_comp_id ADP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id ADP _struct_conn.ptnr2_auth_seq_id 603 _struct_conn.ptnr2_symmetry 1_555 _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 2.174 _struct_conn.pdbx_value_order ? # _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 4TYN _atom_sites.fract_transf_matrix[1][1] 0.011063 _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] 0.007925 _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] 0.018106 _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 3 MG A 1 601 800 MG MG . D 4 BEF A 1 602 900 BEF BEF . E 5 ADP A 1 603 1000 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 . . . E 5 -26.735 30.55 -17.068 1 35.17 ? PB ADP 603 A 1 HETATM 2 O O1B ADP . . . E 5 -27.217 30.746 -18.484 1 35.61 ? O1B ADP 603 A 1 HETATM 3 O O2B ADP . . . E 5 -27.691 31.008 -15.993 1 40.35 ? O2B ADP 603 A 1 HETATM 4 O O3B ADP . . . E 5 -26.129 29.193 -16.799 1 42.81 ? O3B ADP 603 A 1 HETATM 5 P PA ADP . . . E 5 -25.032 32.184 -15.542 1 34.84 ? PA ADP 603 A 1 HETATM 6 O O1A ADP . . . E 5 -25.737 33.5 -15.317 1 47.99 ? O1A ADP 603 A 1 HETATM 7 O O2A ADP . . . E 5 -25.114 31.086 -14.511 1 41.47 ? O2A ADP 603 A 1 HETATM 8 O O3A ADP . . . E 5 -25.508 31.584 -16.957 1 35.96 ? O3A ADP 603 A 1 HETATM 9 O O5' ADP . . . E 5 -23.479 32.482 -15.841 1 41.92 ? O5' ADP 603 A 1 HETATM 10 C C5' ADP . . . E 5 -22.454 31.865 -15.065 1 42.02 ? C5' ADP 603 A 1 HETATM 11 C C4' ADP . . . E 5 -21.164 32.66 -15.206 1 42.41 ? C4' ADP 603 A 1 HETATM 12 O O4' ADP . . . E 5 -21.232 33.49 -16.368 1 37.24 ? O4' ADP 603 A 1 HETATM 13 C C3' ADP . . . E 5 -20.891 33.574 -14.017 1 44.46 ? C3' ADP 603 A 1 HETATM 14 O O3' ADP . . . E 5 -19.747 33.093 -13.301 1 57.71 ? O3' ADP 603 A 1 HETATM 15 C C2' ADP . . . E 5 -20.648 34.953 -14.605 1 42.71 ? C2' ADP 603 A 1 HETATM 16 O O2' ADP . . . E 5 -19.453 35.553 -14.089 1 50.41 ? O2' ADP 603 A 1 HETATM 17 C C1' ADP . . . E 5 -20.545 34.715 -16.108 1 43.17 ? C1' ADP 603 A 1 HETATM 18 N N9 ADP . . . E 5 -21.11 35.83 -16.91 1 39.84 ? N9 ADP 603 A 1 HETATM 19 C C8 ADP . . . E 5 -22.32 36.4 -16.752 1 46.88 ? C8 ADP 603 A 1 HETATM 20 N N7 ADP . . . E 5 -22.504 37.394 -17.657 1 48.68 ? N7 ADP 603 A 1 HETATM 21 C C5 ADP . . . E 5 -21.395 37.467 -18.413 1 46.74 ? C5 ADP 603 A 1 HETATM 22 C C6 ADP . . . E 5 -20.934 38.295 -19.547 1 44.79 ? C6 ADP 603 A 1 HETATM 23 N N6 ADP . . . E 5 -21.736 39.263 -20.048 1 40.57 ? N6 ADP 603 A 1 HETATM 24 N N1 ADP . . . E 5 -19.705 38.051 -20.052 1 46.74 ? N1 ADP 603 A 1 HETATM 25 C C2 ADP . . . E 5 -18.909 37.087 -19.551 1 49.24 ? C2 ADP 603 A 1 HETATM 26 N N3 ADP . . . E 5 -19.271 36.301 -18.519 1 44.47 ? N3 ADP 603 A 1 HETATM 27 C C4 ADP . . . E 5 -20.476 36.438 -17.916 1 44.07 ? C4 ADP 603 A 1 HETATM 28 H "H5'1" ADP . . . E 5 -22.297 30.84 -15.408 1 50.42 ? "H5'1" ADP 603 A 1 HETATM 29 H "H5'2" ADP . . . E 5 -22.755 31.832 -14.015 1 50.42 ? "H5'2" ADP 603 A 1 HETATM 30 H H4' ADP . . . E 5 -20.327 31.954 -15.304 1 50.89 ? H4' ADP 603 A 1 HETATM 31 H H3' ADP . . . E 5 -21.776 33.602 -13.365 1 53.35 ? H3' ADP 603 A 1 HETATM 32 H HO3' ADP . . . E 5 -19.573 33.672 -12.546 1 69.25 ? HO3' ADP 603 A 1 HETATM 33 H H2' ADP . . . E 5 -21.518 35.592 -14.4 1 51.25 ? H2' ADP 603 A 1 HETATM 34 H HO2' ADP . . . E 5 -19.537 35.664 -13.132 1 60.49 ? HO2' ADP 603 A 1 HETATM 35 H H1' ADP . . . E 5 -19.483 34.593 -16.361 1 51.8 ? H1' ADP 603 A 1 HETATM 36 H H8 ADP . . . E 5 -23.045 36.106 -16.003 1 56.25 ? H8 ADP 603 A 1 HETATM 37 H HN61 ADP . . . E 5 -22.65 39.419 -19.648 1 48.69 ? HN61 ADP 603 A 1 HETATM 38 H HN62 ADP . . . E 5 -21.421 39.829 -20.823 1 48.69 ? HN62 ADP 603 A 1 HETATM 39 H H2 ADP . . . E 5 -17.933 36.938 -19.996 1 59.09 ? H2 ADP 603 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #