data_5OEC # _model_server_result.job_id GsLdosMlL8SoYDpa97p8Tw _model_server_result.datetime_utc '2024-11-05 00:31:03' _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 5oec # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":900}' # _entry.id 5OEC # _exptl.entry_id 5OEC _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 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 5OEC _cell.length_a 47.822 _cell.length_b 66.993 _cell.length_c 110.987 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OEC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 # 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 covale ? covale1 A C GLN 79 A GLN 96 1_555 A N MLY 80 A MLY 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MLY 80 A MLY 97 1_555 A N ILE 81 A ILE 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C ILE 90 A ILE 107 1_555 A N MLY 91 A MLY 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MLY 91 A MLY 108 1_555 A N GLU 92 A GLU 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C VAL 145 A VAL 162 1_555 A N MLY 146 A MLY 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 A C MLY 146 A MLY 163 1_555 A N MLY 147 A MLY 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C MLY 147 A MLY 164 1_555 A N VAL 148 A VAL 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B C LEU 46 B LEU 64 1_555 B N MLY 47 B MLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 B C MLY 47 B MLY 65 1_555 B N VAL 48 B VAL 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B C ASP 144 B ASP 162 1_555 B N MLY 145 B MLY 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 B C MLY 145 B MLY 163 1_555 B N GLU 146 B GLU 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 B OG1 THR 21 B THR 39 1_555 D MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 C O1B GDP . B GDP 900 1_555 D MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc3 D MG MG . B MG 901 1_555 F O HOH . B HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 D MG MG . B MG 901 1_555 F O HOH . B HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 D MG MG . B MG 901 1_555 F O HOH . B HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc6 D MG MG . B MG 901 1_555 F O HOH . B HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? # _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 5OEC _atom_sites.fract_transf_matrix[1][1] 0.020911 _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] 0.014927 _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] 0.00901 _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 3 GDP B 1 900 900 GDP GDP . D 4 MG B 1 901 901 MG MG . E 5 HOH A 1 301 29 HOH HOH . E 5 HOH A 2 302 6 HOH HOH . E 5 HOH A 3 303 1 HOH HOH . E 5 HOH A 4 304 3 HOH HOH . E 5 HOH A 5 305 16 HOH HOH . E 5 HOH A 6 306 57 HOH HOH . E 5 HOH A 7 307 25 HOH HOH . E 5 HOH A 8 308 10 HOH HOH . E 5 HOH A 9 309 5 HOH HOH . E 5 HOH A 10 310 45 HOH HOH . E 5 HOH A 11 311 22 HOH HOH . E 5 HOH A 12 312 2 HOH HOH . E 5 HOH A 13 313 12 HOH HOH . E 5 HOH A 14 314 32 HOH HOH . E 5 HOH A 15 315 40 HOH HOH . E 5 HOH A 16 316 43 HOH HOH . E 5 HOH A 17 317 20 HOH HOH . E 5 HOH A 18 318 9 HOH HOH . E 5 HOH A 19 319 4 HOH HOH . E 5 HOH A 20 320 14 HOH HOH . E 5 HOH A 21 321 7 HOH HOH . E 5 HOH A 22 322 34 HOH HOH . E 5 HOH A 23 323 13 HOH HOH . E 5 HOH A 24 324 23 HOH HOH . E 5 HOH A 25 325 46 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 52 HOH HOH . E 5 HOH A 28 328 55 HOH HOH . E 5 HOH A 29 329 31 HOH HOH . E 5 HOH A 30 330 36 HOH HOH . E 5 HOH A 31 331 33 HOH HOH . E 5 HOH A 32 332 30 HOH HOH . F 5 HOH B 1 1001 39 HOH HOH . F 5 HOH B 2 1002 60 HOH HOH . F 5 HOH B 3 1003 27 HOH HOH . F 5 HOH B 4 1004 28 HOH HOH . F 5 HOH B 5 1005 58 HOH HOH . F 5 HOH B 6 1006 51 HOH HOH . F 5 HOH B 7 1007 15 HOH HOH . F 5 HOH B 8 1008 11 HOH HOH . F 5 HOH B 9 1009 56 HOH HOH . F 5 HOH B 10 1010 59 HOH HOH . F 5 HOH B 11 1011 24 HOH HOH . F 5 HOH B 12 1012 19 HOH HOH . F 5 HOH B 13 1013 44 HOH HOH . F 5 HOH B 14 1014 48 HOH HOH . F 5 HOH B 15 1015 8 HOH HOH . F 5 HOH B 16 1016 21 HOH HOH . F 5 HOH B 17 1017 17 HOH HOH . F 5 HOH B 18 1018 18 HOH HOH . F 5 HOH B 19 1019 49 HOH HOH . F 5 HOH B 20 1020 35 HOH HOH . F 5 HOH B 21 1021 41 HOH HOH . F 5 HOH B 22 1022 37 HOH HOH . F 5 HOH B 23 1023 53 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 3 10.723 22.796 148.519 1 48.61 ? PB GDP 900 B 1 HETATM 2 O O1B GDP . . . C 3 11.032 23.232 147.106 1 48.24 ? O1B GDP 900 B 1 HETATM 3 O O2B GDP . . . C 3 11.778 21.829 148.999 1 34.32 ? O2B GDP 900 B 1 HETATM 4 O O3B GDP . . . C 3 9.369 22.128 148.559 1 41.4 ? O3B GDP 900 B 1 HETATM 5 O O3A GDP . . . C 3 10.713 24.079 149.488 1 48.88 ? O3A GDP 900 B 1 HETATM 6 P PA GDP . . . C 3 9.722 25.316 149.215 1 55.42 ? PA GDP 900 B 1 HETATM 7 O O1A GDP . . . C 3 10.431 26.398 148.436 1 57.53 ? O1A GDP 900 B 1 HETATM 8 O O2A GDP . . . C 3 8.469 24.872 148.499 1 53.16 ? O2A GDP 900 B 1 HETATM 9 O O5' GDP . . . C 3 9.38 25.829 150.7 1 64.66 ? O5' GDP 900 B 1 HETATM 10 C C5' GDP . . . C 3 8.032 25.813 151.164 1 61.68 ? C5' GDP 900 B 1 HETATM 11 C C4' GDP . . . C 3 7.814 26.99 152.101 1 58.4 ? C4' GDP 900 B 1 HETATM 12 O O4' GDP . . . C 3 8.885 27.078 153.042 1 56.98 ? O4' GDP 900 B 1 HETATM 13 C C3' GDP . . . C 3 7.794 28.292 151.322 1 63.32 ? C3' GDP 900 B 1 HETATM 14 O O3' GDP . . . C 3 6.486 28.861 151.392 1 67.55 ? O3' GDP 900 B 1 HETATM 15 C C2' GDP . . . C 3 8.799 29.199 152.002 1 61.57 ? C2' GDP 900 B 1 HETATM 16 O O2' GDP . . . C 3 8.183 30.443 152.348 1 69.34 ? O2' GDP 900 B 1 HETATM 17 C C1' GDP . . . C 3 9.233 28.448 153.251 1 57.36 ? C1' GDP 900 B 1 HETATM 18 N N9 GDP . . . C 3 10.695 28.587 153.464 1 61.19 ? N9 GDP 900 B 1 HETATM 19 C C8 GDP . . . C 3 11.663 28.003 152.734 1 65.57 ? C8 GDP 900 B 1 HETATM 20 N N7 GDP . . . C 3 12.895 28.335 153.201 1 65.85 ? N7 GDP 900 B 1 HETATM 21 C C5 GDP . . . C 3 12.721 29.148 154.259 1 66.16 ? C5 GDP 900 B 1 HETATM 22 C C6 GDP . . . C 3 13.599 29.862 155.216 1 67.12 ? C6 GDP 900 B 1 HETATM 23 O O6 GDP . . . C 3 14.843 29.774 155.138 1 60.04 ? O6 GDP 900 B 1 HETATM 24 N N1 GDP . . . C 3 13.018 30.602 156.17 1 76.62 ? N1 GDP 900 B 1 HETATM 25 C C2 GDP . . . C 3 11.68 30.714 156.28 1 76.53 ? C2 GDP 900 B 1 HETATM 26 N N2 GDP . . . C 3 11.173 31.484 157.274 1 80.43 ? N2 GDP 900 B 1 HETATM 27 N N3 GDP . . . C 3 10.817 30.089 155.439 1 71.84 ? N3 GDP 900 B 1 HETATM 28 C C4 GDP . . . C 3 11.27 29.309 154.43 1 67.45 ? C4 GDP 900 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #