data_2QMU # _model_server_result.job_id 5FsXn8aUnRLso8-puTsEdQ _model_server_result.datetime_utc '2024-10-13 00:23:57' _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 2qmu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":417}' # _entry.id 2QMU # _exptl.entry_id 2QMU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 120 _cell.entry_id 2QMU _cell.length_a 118.323 _cell.length_b 118.323 _cell.length_c 161.449 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QMU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 107.632667 # _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 # 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 58 A CYS 59 1_555 A SG CYS 73 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? disulf ? disulf2 A SG CYS 61 A CYS 62 1_555 A SG CYS 76 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc1 C SG CYS 105 C CYS 106 1_555 F ZN ZN . C ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc2 C SG CYS 108 C CYS 109 1_555 F ZN ZN . C ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 C SG CYS 126 C CYS 127 1_555 F ZN ZN . C ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc4 C SG CYS 129 C CYS 130 1_555 F ZN ZN . C ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2QMU _atom_sites.fract_transf_matrix[1][1] 0.008451 _atom_sites.fract_transf_matrix[1][2] 0.004879 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009759 _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] 0.006194 _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 D 4 PO4 A 1 416 413 PO4 PO4 . E 5 GDP A 1 417 412 GDP GDP . F 6 ZN C 1 414 414 ZN ZN . G 7 HOH A 1 418 415 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 GDP . . . E 5 -39.492 50.582 54.097 1 64.53 ? PB GDP 417 A 1 HETATM 2 O O1B GDP . . . E 5 -38.389 51.476 54.431 1 67.58 ? O1B GDP 417 A 1 HETATM 3 O O2B GDP . . . E 5 -40.774 51.227 53.734 1 64.94 ? O2B GDP 417 A 1 HETATM 4 O O3B GDP . . . E 5 -39.338 49.696 52.842 1 61.94 ? O3B GDP 417 A 1 HETATM 5 O O3A GDP . . . E 5 -39.932 49.774 55.56 1 65.77 ? O3A GDP 417 A 1 HETATM 6 P PA GDP . . . E 5 -38.871 48.847 56.456 1 66.96 ? PA GDP 417 A 1 HETATM 7 O O1A GDP . . . E 5 -39.682 47.602 56.531 1 67.62 ? O1A GDP 417 A 1 HETATM 8 O O2A GDP . . . E 5 -37.459 48.667 56.052 1 67.49 ? O2A GDP 417 A 1 HETATM 9 O O5' GDP . . . E 5 -39.09 49.606 57.881 1 65.46 ? O5' GDP 417 A 1 HETATM 10 C C5' GDP . . . E 5 -38.523 50.858 58.3 1 62.61 ? C5' GDP 417 A 1 HETATM 11 C C4' GDP . . . E 5 -38.003 50.802 59.776 1 61.95 ? C4' GDP 417 A 1 HETATM 12 O O4' GDP . . . E 5 -38.995 50.926 60.87 1 62.23 ? O4' GDP 417 A 1 HETATM 13 C C3' GDP . . . E 5 -37.288 49.498 60.215 1 62 ? C3' GDP 417 A 1 HETATM 14 O O3' GDP . . . E 5 -36.358 49.95 61.243 1 61.75 ? O3' GDP 417 A 1 HETATM 15 C C2' GDP . . . E 5 -38.409 48.647 60.828 1 62.19 ? C2' GDP 417 A 1 HETATM 16 O O2' GDP . . . E 5 -37.963 47.61 61.692 1 60.52 ? O2' GDP 417 A 1 HETATM 17 C C1' GDP . . . E 5 -39.233 49.689 61.538 1 64.23 ? C1' GDP 417 A 1 HETATM 18 N N9 GDP . . . E 5 -40.72 49.413 61.492 1 69.17 ? N9 GDP 417 A 1 HETATM 19 C C8 GDP . . . E 5 -41.537 48.922 60.503 1 71.41 ? C8 GDP 417 A 1 HETATM 20 N N7 GDP . . . E 5 -42.787 48.83 60.851 1 72.29 ? N7 GDP 417 A 1 HETATM 21 C C5 GDP . . . E 5 -42.829 49.269 62.163 1 72.2 ? C5 GDP 417 A 1 HETATM 22 C C6 GDP . . . E 5 -43.914 49.426 63.09 1 73.07 ? C6 GDP 417 A 1 HETATM 23 O O6 GDP . . . E 5 -45.113 49.151 62.913 1 74.62 ? O6 GDP 417 A 1 HETATM 24 N N1 GDP . . . E 5 -43.483 49.926 64.344 1 73.36 ? N1 GDP 417 A 1 HETATM 25 C C2 GDP . . . E 5 -42.187 50.266 64.667 1 72.49 ? C2 GDP 417 A 1 HETATM 26 N N2 GDP . . . E 5 -42.001 50.725 65.898 1 72.44 ? N2 GDP 417 A 1 HETATM 27 N N3 GDP . . . E 5 -41.146 50.138 63.798 1 72.22 ? N3 GDP 417 A 1 HETATM 28 C C4 GDP . . . E 5 -41.555 49.652 62.593 1 71.09 ? C4 GDP 417 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #