data_5DGM # _model_server_result.job_id qjmkb6MXVf1-BC6RzZmFtg _model_server_result.datetime_utc '2025-02-05 17:46:01' _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 5dgm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5DGM # _exptl.entry_id 5DGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE ION' _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 5DGM _cell.length_a 110.723 _cell.length_b 110.723 _cell.length_c 76.775 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DGM _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 110.723 110.723 38.3875 # _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 # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _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 P O1 PO4 doub 302 n n P O2 PO4 sing 303 n n P O3 PO4 sing 304 n n P O4 PO4 sing 305 n n # _atom_sites.entry_id 5DGM _atom_sites.fract_transf_matrix[1][1] 0.009032 _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] 0.009032 _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] 0.013025 _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 59Z F 1 401 1 59Z LIG . C 3 PO4 F 1 402 1 PO4 PO4 . D 4 HOH F 1 501 5 HOH HOH . D 4 HOH F 2 502 20 HOH HOH . D 4 HOH F 3 503 26 HOH HOH . D 4 HOH F 4 504 31 HOH HOH . D 4 HOH F 5 505 8 HOH HOH . D 4 HOH F 6 506 14 HOH HOH . D 4 HOH F 7 507 17 HOH HOH . D 4 HOH F 8 508 11 HOH HOH . D 4 HOH F 9 509 10 HOH HOH . D 4 HOH F 10 510 29 HOH HOH . D 4 HOH F 11 511 1 HOH HOH . D 4 HOH F 12 512 12 HOH HOH . D 4 HOH F 13 513 9 HOH HOH . D 4 HOH F 14 514 19 HOH HOH . D 4 HOH F 15 515 2 HOH HOH . D 4 HOH F 16 516 15 HOH HOH . D 4 HOH F 17 517 27 HOH HOH . D 4 HOH F 18 518 25 HOH HOH . D 4 HOH F 19 519 6 HOH HOH . D 4 HOH F 20 520 30 HOH HOH . D 4 HOH F 21 521 23 HOH HOH . D 4 HOH F 22 522 32 HOH HOH . D 4 HOH F 23 523 21 HOH HOH . D 4 HOH F 24 524 4 HOH HOH . D 4 HOH F 25 525 22 HOH HOH . D 4 HOH F 26 526 16 HOH HOH . D 4 HOH F 27 527 33 HOH HOH . D 4 HOH F 28 528 13 HOH HOH . D 4 HOH F 29 529 18 HOH HOH . D 4 HOH F 30 530 28 HOH HOH . D 4 HOH F 31 531 24 HOH HOH . D 4 HOH F 32 532 3 HOH HOH . D 4 HOH F 33 533 7 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 P PO4 . . . C 3 9.157 73.984 22.671 1 104.98 ? P PO4 402 F 1 HETATM 2 O O1 PO4 . . . C 3 9.909 74.303 21.35 1 103.7 ? O1 PO4 402 F 1 HETATM 3 O O2 PO4 . . . C 3 10.067 74.462 23.855 1 103.71 ? O2 PO4 402 F 1 HETATM 4 O O3 PO4 . . . C 3 8.907 72.442 22.772 1 105.42 ? O3 PO4 402 F 1 HETATM 5 O O4 PO4 . . . C 3 7.759 74.724 22.713 1 105.31 ? O4 PO4 402 F 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 5 #