data_5MI9 # _model_server_result.job_id rT_X8KezD6P-cbirZlwH-g _model_server_result.datetime_utc '2024-11-23 10:25:11' _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 5mi9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5MI9 # _exptl.entry_id 5MI9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 109.25 _cell.angle_beta 106 _cell.angle_gamma 88.15 _cell.entry_id 5MI9 _cell.length_a 58.12 _cell.length_b 62.1 _cell.length_c 65.47 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MI9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 D 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 metalc ? metalc1 A OG1 THR 34 A THR 26 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc2 C MG MG . A MG 401 1_555 D O3B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc3 C MG MG . A MG 401 1_555 D O2B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc4 C MG MG . A MG 401 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc5 C MG MG . A MG 401 1_555 G O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc7 B OG1 THR 34 B THR 26 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc8 E MG MG . B MG 401 1_555 F O1B GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc9 E MG MG . B MG 401 1_555 F O1A GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc10 E MG MG . B MG 401 1_555 F O2A GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc11 E MG MG . B MG 401 1_555 H O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc12 E MG MG . B MG 401 1_555 H O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? # _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 5MI9 _atom_sites.fract_transf_matrix[1][1] 0.017206 _atom_sites.fract_transf_matrix[1][2] -0.000556 _atom_sites.fract_transf_matrix[1][3] 0.005037 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016111 _atom_sites.fract_transf_matrix[2][3] 0.005707 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016857 _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 2 MG A 1 401 1 MG MG . D 3 GDP A 1 402 1 GDP GDP . E 2 MG B 1 401 2 MG MG . F 3 GDP B 1 402 2 GDP GDP . G 4 HOH A 1 501 9 HOH HOH . G 4 HOH A 2 502 10 HOH HOH . G 4 HOH A 3 503 8 HOH HOH . G 4 HOH A 4 504 1 HOH HOH . G 4 HOH A 5 505 11 HOH HOH . H 4 HOH B 1 501 2 HOH HOH . H 4 HOH B 2 502 5 HOH HOH . H 4 HOH B 3 503 7 HOH HOH . H 4 HOH B 4 504 6 HOH HOH . H 4 HOH B 5 505 3 HOH HOH . H 4 HOH B 6 506 4 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 . . . D 3 -44.529 0.227 12.053 1 70.51 ? PB GDP 402 A 1 HETATM 2 O O1B GDP . . . D 3 -45.388 0.525 10.788 1 73.36 ? O1B GDP 402 A 1 HETATM 3 O O2B GDP . . . D 3 -42.991 0.488 11.79 1 66.52 ? O2B GDP 402 A 1 HETATM 4 O O3B GDP . . . D 3 -44.821 -1.173 12.519 1 70.57 ? O3B GDP 402 A 1 HETATM 5 O O3A GDP . . . D 3 -45.178 1.119 13.207 1 69.11 ? O3A GDP 402 A 1 HETATM 6 P PA GDP . . . D 3 -45.339 0.869 14.773 1 74.14 ? PA GDP 402 A 1 HETATM 7 O O1A GDP . . . D 3 -46.226 -0.293 14.997 1 74.74 ? O1A GDP 402 A 1 HETATM 8 O O2A GDP . . . D 3 -43.984 0.569 15.462 1 72.08 ? O2A GDP 402 A 1 HETATM 9 O O5' GDP . . . D 3 -45.947 2.242 15.383 1 81.36 ? O5' GDP 402 A 1 HETATM 10 C C5' GDP . . . D 3 -45.413 3.58 15.213 1 84.94 ? C5' GDP 402 A 1 HETATM 11 C C4' GDP . . . D 3 -45.762 4.501 16.363 1 89.4 ? C4' GDP 402 A 1 HETATM 12 O O4' GDP . . . D 3 -47.141 4.936 16.282 1 91.84 ? O4' GDP 402 A 1 HETATM 13 C C3' GDP . . . D 3 -45.567 3.917 17.762 1 94.71 ? C3' GDP 402 A 1 HETATM 14 O O3' GDP . . . D 3 -44.909 4.811 18.65 1 97.58 ? O3' GDP 402 A 1 HETATM 15 C C2' GDP . . . D 3 -46.991 3.57 18.199 1 97.27 ? C2' GDP 402 A 1 HETATM 16 O O2' GDP . . . D 3 -47.186 3.518 19.609 1 98.88 ? O2' GDP 402 A 1 HETATM 17 C C1' GDP . . . D 3 -47.819 4.651 17.493 1 96.6 ? C1' GDP 402 A 1 HETATM 18 N N9 GDP . . . D 3 -49.174 4.166 17.172 1 100.81 ? N9 GDP 402 A 1 HETATM 19 C C8 GDP . . . D 3 -49.482 2.851 16.952 1 103.31 ? C8 GDP 402 A 1 HETATM 20 N N7 GDP . . . D 3 -50.763 2.603 16.882 1 105.77 ? N7 GDP 402 A 1 HETATM 21 C C5 GDP . . . D 3 -51.355 3.842 17.047 1 106.19 ? C5 GDP 402 A 1 HETATM 22 C C6 GDP . . . D 3 -52.749 4.22 17.134 1 106.31 ? C6 GDP 402 A 1 HETATM 23 O O6 GDP . . . D 3 -53.733 3.481 17.068 1 102 ? O6 GDP 402 A 1 HETATM 24 N N1 GDP . . . D 3 -52.897 5.578 17.371 1 109.69 ? N1 GDP 402 A 1 HETATM 25 C C2 GDP . . . D 3 -51.863 6.48 17.509 1 110.05 ? C2 GDP 402 A 1 HETATM 26 N N2 GDP . . . D 3 -52.2 7.743 17.797 1 109.2 ? N2 GDP 402 A 1 HETATM 27 N N3 GDP . . . D 3 -50.571 6.147 17.417 1 109.03 ? N3 GDP 402 A 1 HETATM 28 C C4 GDP . . . D 3 -50.384 4.825 17.207 1 105.21 ? C4 GDP 402 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 229 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #