data_5N6O # _model_server_result.job_id YzkahiU_30uu0LOwecsEIA _model_server_result.datetime_utc '2024-12-21 18:59:34' _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":"C","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 . . . C 2 -11.854 -6.295 13.331 1 24.55 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 2 -11.99 -5.754 11.921 1 24.29 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 2 -11.219 -5.214 14.201 1 27.74 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 2 -13.105 -6.829 13.858 1 23.58 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 2 -10.786 -7.475 13.286 1 24.94 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 2 -9.542 -7.862 14.201 1 24.48 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 2 -8.541 -6.761 14.218 1 23.11 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 2 -10.106 -8.096 15.595 1 25.22 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 2 -8.972 -9.255 13.662 1 24.52 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 2 -9.837 -10.152 12.944 1 28.42 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 2 -9.212 -11.512 12.753 1 31.11 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 2 -8.282 -11.467 11.65 1 32.61 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 2 -8.422 -12.067 13.933 1 32.41 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 2 -8.513 -13.488 13.972 1 34.07 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 2 -6.996 -11.61 13.619 1 31.23 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 2 -6.022 -12.432 14.25 1 31.53 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 2 -6.971 -11.756 12.099 1 31.44 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 2 -6.066 -10.835 11.411 1 31.87 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 2 -6.136 -9.467 11.435 1 32.21 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 2 -5.381 -8.879 10.535 1 31.01 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 2 -4.765 -9.929 9.88 1 31.18 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 2 -3.905 -9.95 8.74 1 30.56 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 2 -3.456 -8.983 8.132 1 31.02 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 2 -3.599 -11.238 8.338 1 31.4 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 2 -4.027 -12.387 8.959 1 30.84 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 2 -3.641 -13.543 8.422 1 29.64 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 2 -4.813 -12.392 10.037 1 31.79 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 2 -5.161 -11.147 10.43 1 32.67 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . C 2 -10.808 -10.207 13.434 1 28.9 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . C 2 -9.979 -9.632 11.998 1 28.23 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . C 2 -9.968 -12.217 12.409 1 30.96 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . C 2 -8.787 -11.669 14.878 1 32.69 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . C 2 -8.726 -13.744 14.908 1 34.06 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . C 2 -6.853 -10.571 13.908 1 31.37 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . C 2 -6.287 -13.368 14.046 1 31.87 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . C 2 -6.726 -12.772 11.792 1 31.23 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . C 2 -6.757 -8.925 12.145 1 32.46 ? H8 GDP 201 A 1 HETATM 38 H HN1 GDP . . . C 2 -3.029 -11.295 7.502 1 31.69 ? HN1 GDP 201 A 1 HETATM 39 H HN21 GDP . . . C 2 -3.931 -14.421 8.841 1 30.03 ? HN21 GDP 201 A 1 HETATM 40 H HN22 GDP . . . C 2 -3.057 -13.617 7.597 1 29.35 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 494 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #