data_5YH2 # _model_server_result.job_id GFDS4dmryPyhA797gxTrBA _model_server_result.datetime_utc '2024-11-15 04:03:49' _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 5yh2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 5YH2 # _exptl.entry_id 5YH2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ATP _entity.formula_weight 507.181 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 5YH2 _cell.length_a 110.059 _cell.length_b 110.059 _cell.length_c 461.698 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YH2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 E N N ? 3 F N 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 disulf ? disulf1 A SG CYS 147 A CYS 209 1_555 A SG CYS 257 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 149 A CYS 211 1_555 A SG CYS 261 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 252 A CYS 314 1_555 A SG CYS 268 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 316 A CYS 378 1_555 A SG CYS 390 A CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 391 A CYS 453 1_555 A SG CYS 450 A CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 338 C CYS 338 1_555 B SG CYS 354 C CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 343 C CYS 343 1_555 B SG CYS 347 C CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 402 C CYS 402 1_555 B SG CYS 476 C CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 477 C CYS 477 1_555 B SG CYS 536 C CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf10 C SG CYS 147 B CYS 209 1_555 C SG CYS 257 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 C SG CYS 149 B CYS 211 1_555 C SG CYS 261 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf12 C SG CYS 252 B CYS 314 1_555 C SG CYS 268 B CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 C SG CYS 316 B CYS 378 1_555 C SG CYS 390 B CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf14 C SG CYS 391 B CYS 453 1_555 C SG CYS 450 B CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 D SG CYS 338 D CYS 338 1_555 D SG CYS 354 D CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 D SG CYS 343 D CYS 343 1_555 D SG CYS 347 D CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 D SG CYS 402 D CYS 402 1_555 D SG CYS 476 D CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 D SG CYS 477 D CYS 477 1_555 D SG CYS 536 D CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YH2 _atom_sites.fract_transf_matrix[1][1] 0.009086 _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] 0.009086 _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] 0.002166 _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 E 3 ATP A 1 701 701 ATP ATP . F 3 ATP B 1 701 701 ATP ATP . # 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 PG ATP . . . F 3 -34.768 13.088 -117.524 1 75.24 ? PG ATP 701 B 1 HETATM 2 O O1G ATP . . . F 3 -34.668 13.025 -119.03 1 69.81 ? O1G ATP 701 B 1 HETATM 3 O O2G ATP . . . F 3 -34.28 14.367 -116.879 1 58.38 ? O2G ATP 701 B 1 HETATM 4 O O3G ATP . . . F 3 -34.268 11.836 -116.844 1 78.18 ? O3G ATP 701 B 1 HETATM 5 P PB ATP . . . F 3 -37.326 11.876 -117.18 1 74.16 ? PB ATP 701 B 1 HETATM 6 O O1B ATP . . . F 3 -38.498 12.045 -118.11 1 68.91 ? O1B ATP 701 B 1 HETATM 7 O O2B ATP . . . F 3 -36.536 10.587 -117.223 1 64.75 ? O2B ATP 701 B 1 HETATM 8 O O3B ATP . . . F 3 -36.354 13.157 -117.246 1 77.5 ? O3B ATP 701 B 1 HETATM 9 P PA ATP . . . F 3 -38.666 10.998 -114.936 1 82.59 ? PA ATP 701 B 1 HETATM 10 O O1A ATP . . . F 3 -38.595 9.759 -115.792 1 75.64 ? O1A ATP 701 B 1 HETATM 11 O O2A ATP . . . F 3 -38.138 11.001 -113.521 1 88.28 ? O2A ATP 701 B 1 HETATM 12 O O3A ATP . . . F 3 -37.928 12.172 -115.726 1 69.61 ? O3A ATP 701 B 1 HETATM 13 O O5' ATP . . . F 3 -40.19 11.507 -114.98 1 64.31 ? O5' ATP 701 B 1 HETATM 14 C C5' ATP . . . F 3 -41.17 10.681 -115.603 1 62.18 ? C5' ATP 701 B 1 HETATM 15 C C4' ATP . . . F 3 -42.344 10.452 -114.663 1 61.08 ? C4' ATP 701 B 1 HETATM 16 O O4' ATP . . . F 3 -43.533 10.365 -115.444 1 61.39 ? O4' ATP 701 B 1 HETATM 17 C C3' ATP . . . F 3 -42.196 9.151 -113.886 1 58.94 ? C3' ATP 701 B 1 HETATM 18 O O3' ATP . . . F 3 -42.199 9.406 -112.477 1 54.69 ? O3' ATP 701 B 1 HETATM 19 C C2' ATP . . . F 3 -43.404 8.314 -114.249 1 60.97 ? C2' ATP 701 B 1 HETATM 20 O O2' ATP . . . F 3 -44.097 7.923 -113.061 1 69.04 ? O2' ATP 701 B 1 HETATM 21 C C1' ATP . . . F 3 -44.297 9.22 -115.078 1 59.58 ? C1' ATP 701 B 1 HETATM 22 N N9 ATP . . . F 3 -44.742 8.541 -116.313 1 54.38 ? N9 ATP 701 B 1 HETATM 23 C C8 ATP . . . F 3 -44.233 8.727 -117.544 1 49.61 ? C8 ATP 701 B 1 HETATM 24 N N7 ATP . . . F 3 -44.878 7.957 -118.454 1 45.2 ? N7 ATP 701 B 1 HETATM 25 C C5 ATP . . . F 3 -45.824 7.264 -117.795 1 49.94 ? C5 ATP 701 B 1 HETATM 26 C C6 ATP . . . F 3 -46.863 6.269 -118.146 1 57.59 ? C6 ATP 701 B 1 HETATM 27 N N6 ATP . . . F 3 -47.028 5.843 -119.423 1 55.38 ? N6 ATP 701 B 1 HETATM 28 N N1 ATP . . . F 3 -47.644 5.798 -117.146 1 63.74 ? N1 ATP 701 B 1 HETATM 29 C C2 ATP . . . F 3 -47.496 6.208 -115.871 1 61.29 ? C2 ATP 701 B 1 HETATM 30 N N3 ATP . . . F 3 -46.576 7.107 -115.483 1 58.09 ? N3 ATP 701 B 1 HETATM 31 C C4 ATP . . . F 3 -45.73 7.658 -116.383 1 53.07 ? C4 ATP 701 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #