data_8AFC # _model_server_result.job_id '_dhuHnghs5R_F38DjX6VTw' _model_server_result.datetime_utc '2024-10-19 15:37:29' _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 8afc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 8AFC # _exptl.entry_id 8AFC _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 120 _cell.entry_id 8AFC _cell.length_a 136.04 _cell.length_b 136.04 _cell.length_c 91.26 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AFC _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # 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,E,F,H 1 1 B,G,I 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 G 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 disulf ? disulf1 A SG CYS 12 A CYS 12 1_555 B SG CYS 12 B CYS 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc2 C O1B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc3 D MG MG . A MG 202 1_555 H O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc4 D MG MG . A MG 202 1_555 H O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc5 D MG MG . A MG 202 1_555 H O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc6 D MG MG . A MG 202 1_555 H O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? # _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 8AFC _atom_sites.fract_transf_matrix[1][1] 0.007351 _atom_sites.fract_transf_matrix[1][2] 0.004244 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008488 _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] 0.010958 _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 1 201 201 GDP GDP . D 3 MG A 1 202 202 MG MG . E 4 LXK A 1 203 1 LXK LIG . F 5 SO4 A 1 204 1 SO4 SO4 . G 2 GDP B 1 201 201 GDP GDP . H 6 HOH A 1 301 19 HOH HOH . H 6 HOH A 2 302 1 HOH HOH . H 6 HOH A 3 303 24 HOH HOH . H 6 HOH A 4 304 13 HOH HOH . H 6 HOH A 5 305 16 HOH HOH . H 6 HOH A 6 306 22 HOH HOH . H 6 HOH A 7 307 6 HOH HOH . H 6 HOH A 8 308 37 HOH HOH . H 6 HOH A 9 309 15 HOH HOH . H 6 HOH A 10 310 12 HOH HOH . H 6 HOH A 11 311 14 HOH HOH . H 6 HOH A 12 312 39 HOH HOH . H 6 HOH A 13 313 10 HOH HOH . H 6 HOH A 14 314 20 HOH HOH . H 6 HOH A 15 315 34 HOH HOH . H 6 HOH A 16 316 5 HOH HOH . H 6 HOH A 17 317 36 HOH HOH . H 6 HOH A 18 318 18 HOH HOH . H 6 HOH A 19 319 23 HOH HOH . H 6 HOH A 20 320 7 HOH HOH . H 6 HOH A 21 321 38 HOH HOH . H 6 HOH A 22 322 26 HOH HOH . H 6 HOH A 23 323 31 HOH HOH . H 6 HOH A 24 324 35 HOH HOH . H 6 HOH A 25 325 43 HOH HOH . H 6 HOH A 26 326 17 HOH HOH . I 6 HOH B 1 301 41 HOH HOH . I 6 HOH B 2 302 33 HOH HOH . I 6 HOH B 3 303 30 HOH HOH . I 6 HOH B 4 304 29 HOH HOH . I 6 HOH B 5 305 40 HOH HOH . I 6 HOH B 6 306 3 HOH HOH . I 6 HOH B 7 307 8 HOH HOH . I 6 HOH B 8 308 21 HOH HOH . I 6 HOH B 9 309 9 HOH HOH . I 6 HOH B 10 310 2 HOH HOH . I 6 HOH B 11 311 11 HOH HOH . I 6 HOH B 12 312 42 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 . . . G 2 -14.611 63.57 -7.467 1 44.9 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . G 2 -15.185 62.435 -8.232 1 47.26 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . G 2 -14.393 63.346 -5.955 1 46.44 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . G 2 -15.368 64.878 -7.625 1 43.61 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . G 2 -13.167 63.909 -8.041 1 50.16 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . G 2 -11.689 63.436 -7.686 1 46.59 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . G 2 -11.716 61.921 -7.686 1 48.63 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . G 2 -11.264 64.028 -6.416 1 43.76 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . G 2 -10.847 63.86 -8.976 1 52.3 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . G 2 -11.065 63.317 -10.304 1 47.61 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . G 2 -9.788 63.512 -11.081 1 50.31 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . G 2 -9.518 64.924 -11.245 1 52.23 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . G 2 -8.543 62.903 -10.429 1 52.39 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . G 2 -7.765 62.176 -11.365 1 52.91 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . G 2 -7.838 64.109 -9.799 1 50.79 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . G 2 -6.429 63.962 -9.734 1 51.71 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . G 2 -8.216 65.223 -10.766 1 49.95 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . G 2 -8.244 66.547 -10.142 1 45.97 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . G 2 -9.033 66.979 -9.104 1 43.39 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . G 2 -8.873 68.25 -8.812 1 43.63 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . G 2 -7.917 68.69 -9.719 1 45.7 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . G 2 -7.357 70.007 -9.99 1 46.63 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . G 2 -7.609 71.061 -9.409 1 50.48 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . G 2 -6.474 69.997 -11.056 1 41.14 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . G 2 -6.126 68.892 -11.78 1 42.92 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . G 2 -5.259 69.072 -12.775 1 47.94 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . G 2 -6.621 67.676 -11.556 1 44.64 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . G 2 -7.511 67.643 -10.538 1 46.92 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #