data_5N6O # _model_server_result.job_id 1RJ7AHWqtboXAFoVqToiHA _model_server_result.datetime_utc '2024-12-22 01:18:26' _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 5n6o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5N6O # _exptl.entry_id 5N6O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5N6O _cell.length_a 41.641 _cell.length_b 82.656 _cell.length_c 105.898 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N6O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,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 ? 2 C N N ? 2 E 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 16 A THR 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc2 C O2B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc3 D MG MG . A MG 202 1_555 G O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc4 D MG MG . A MG 202 1_555 G O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc5 D MG MG . A MG 202 1_555 G O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc6 D MG MG . A MG 202 1_555 G O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc7 B OG1 THR 16 B THR 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc8 E O1B GDP . B GDP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc9 F MG MG . B MG 202 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc10 F MG MG . B MG 202 1_555 H O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc11 F MG MG . B MG 202 1_555 H O HOH . B HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc12 F MG MG . B MG 202 1_555 H O HOH . B HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? # _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 5N6O _atom_sites.fract_transf_matrix[1][1] 0.024015 _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] 0.012098 _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] 0.009443 _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 GDP A 1 201 1 GDP GDP . D 3 MG A 1 202 2 MG MG . E 2 GDP B 1 201 2 GDP GDP . F 3 MG B 1 202 1 MG MG . G 4 HOH A 1 301 104 HOH HOH . G 4 HOH A 2 302 99 HOH HOH . G 4 HOH A 3 303 95 HOH HOH . G 4 HOH A 4 304 9 HOH HOH . G 4 HOH A 5 305 92 HOH HOH . G 4 HOH A 6 306 20 HOH HOH . G 4 HOH A 7 307 29 HOH HOH . G 4 HOH A 8 308 88 HOH HOH . G 4 HOH A 9 309 23 HOH HOH . G 4 HOH A 10 310 3 HOH HOH . G 4 HOH A 11 311 33 HOH HOH . G 4 HOH A 12 312 101 HOH HOH . G 4 HOH A 13 313 91 HOH HOH . G 4 HOH A 14 314 94 HOH HOH . G 4 HOH A 15 315 73 HOH HOH . G 4 HOH A 16 316 97 HOH HOH . G 4 HOH A 17 317 45 HOH HOH . G 4 HOH A 18 318 52 HOH HOH . G 4 HOH A 19 319 69 HOH HOH . G 4 HOH A 20 320 39 HOH HOH . G 4 HOH A 21 321 35 HOH HOH . G 4 HOH A 22 322 103 HOH HOH . G 4 HOH A 23 323 59 HOH HOH . H 4 HOH B 1 301 98 HOH HOH . H 4 HOH B 2 302 36 HOH HOH . H 4 HOH B 3 303 6 HOH HOH . H 4 HOH B 4 304 64 HOH HOH . H 4 HOH B 5 305 17 HOH HOH . H 4 HOH B 6 306 13 HOH HOH . H 4 HOH B 7 307 22 HOH HOH . H 4 HOH B 8 308 51 HOH HOH . H 4 HOH B 9 309 5 HOH HOH . H 4 HOH B 10 310 25 HOH HOH . H 4 HOH B 11 311 46 HOH HOH . H 4 HOH B 12 312 62 HOH HOH . H 4 HOH B 13 313 8 HOH HOH . H 4 HOH B 14 314 96 HOH HOH . H 4 HOH B 15 315 50 HOH HOH . H 4 HOH B 16 316 93 HOH HOH . H 4 HOH B 17 317 1 HOH HOH . H 4 HOH B 18 318 18 HOH HOH . H 4 HOH B 19 319 43 HOH HOH . H 4 HOH B 20 320 74 HOH HOH . H 4 HOH B 21 321 102 HOH HOH . H 4 HOH B 22 322 65 HOH HOH . H 4 HOH B 23 323 100 HOH HOH . H 4 HOH B 24 324 32 HOH HOH . H 4 HOH B 25 325 10 HOH HOH . H 4 HOH B 26 326 12 HOH HOH . H 4 HOH B 27 327 67 HOH HOH . H 4 HOH B 28 328 40 HOH HOH . H 4 HOH B 29 329 84 HOH HOH . H 4 HOH B 30 330 76 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 2 8.837 4.136 -24.003 1 25.92 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . E 2 9.48 3.396 -25.186 1 24.78 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . E 2 7.615 4.819 -24.584 1 28.01 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . E 2 8.504 3.271 -22.805 1 22.69 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . E 2 9.85 5.303 -23.62 1 26.79 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . E 2 11.126 5.854 -24.397 1 29.35 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . E 2 10.682 6.569 -25.651 1 26.03 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . E 2 12.043 4.73 -24.709 1 30.43 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . E 2 11.705 6.987 -23.467 1 32 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . E 2 10.78 7.937 -22.91 1 33.34 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . E 2 11.531 9.155 -22.443 1 32.3 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . E 2 12.374 8.792 -21.33 1 29.83 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . E 2 12.433 9.818 -23.482 1 32.19 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . E 2 12.365 11.241 -23.418 1 33.72 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . E 2 13.819 9.271 -23.138 1 32.08 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . E 2 14.826 10.21 -23.514 1 34.33 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . E 2 13.725 9.077 -21.62 1 28.95 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . E 2 14.531 7.962 -21.099 1 26.78 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . E 2 14.446 6.639 -21.46 1 26.35 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . E 2 15.246 5.85 -20.782 1 24.03 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . E 2 15.905 6.703 -19.916 1 24.57 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . E 2 16.889 6.45 -18.901 1 24.3 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . E 2 17.377 5.36 -18.595 1 24.56 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . E 2 17.265 7.608 -18.238 1 21.81 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . E 2 16.781 8.863 -18.501 1 20.85 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . E 2 17.33 9.874 -17.831 1 23.48 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . E 2 15.862 9.118 -19.431 1 21.77 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . E 2 15.473 8.013 -20.099 1 24.79 ? C4 GDP 201 B 1 HETATM 29 H H5' GDP . . . E 2 9.979 8.17 -23.61 1 33.32 ? H5' GDP 201 B 1 HETATM 30 H "H5''" GDP . . . E 2 10.343 7.392 -22.076 1 33.14 ? "H5''" GDP 201 B 1 HETATM 31 H H4' GDP . . . E 2 10.83 9.868 -22.011 1 32.63 ? H4' GDP 201 B 1 HETATM 32 H H3' GDP . . . E 2 12.142 9.525 -24.489 1 32.43 ? H3' GDP 201 B 1 HETATM 33 H HO3' GDP . . . E 2 11.565 11.519 -23.938 1 33.63 ? HO3' GDP 201 B 1 HETATM 34 H H2' GDP . . . E 2 13.97 8.318 -23.64 1 32.47 ? H2' GDP 201 B 1 HETATM 35 H HO2' GDP . . . E 2 15.59 10.066 -22.896 1 34.5 ? HO2' GDP 201 B 1 HETATM 36 H H1' GDP . . . E 2 13.998 9.982 -21.08 1 29.07 ? H1' GDP 201 B 1 HETATM 37 H H8 GDP . . . E 2 13.779 6.267 -22.236 1 26.16 ? H8 GDP 201 B 1 HETATM 38 H HN1 GDP . . . E 2 17.969 7.477 -17.52 1 21.72 ? HN1 GDP 201 B 1 HETATM 39 H HN21 GDP . . . E 2 17.001 10.822 -17.984 1 23.74 ? HN21 GDP 201 B 1 HETATM 40 H HN22 GDP . . . E 2 18.097 9.772 -17.174 1 23.7 ? HN22 GDP 201 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #