data_8ZB8 # _model_server_result.job_id j84O3_F5K43bjw38vugtfg _model_server_result.datetime_utc '2024-11-14 19:06:20' _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 8zb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":501}' # _entry.id 8ZB8 # _exptl.entry_id 8ZB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 8ZB8 _cell.length_a 105.599 _cell.length_b 158.202 _cell.length_c 180.521 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ZB8 _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 9 K N N ? 9 R 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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc6 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc7 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc9 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc10 K O2A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc17 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc18 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? # _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 175 n n PB O2B GDP sing 176 n n PB O3B GDP sing 177 n n PB O3A GDP sing 178 n n O2B HOB2 GDP sing 179 n n O3B HOB3 GDP sing 180 n n O3A PA GDP sing 181 n n PA O1A GDP doub 182 n n PA O2A GDP sing 183 n n PA O5' GDP sing 184 n n O2A HOA2 GDP sing 185 n n O5' C5' GDP sing 186 n n C5' C4' GDP sing 187 n n C5' H5' GDP sing 188 n n C5' "H5''" GDP sing 189 n n C4' O4' GDP sing 190 n n C4' C3' GDP sing 191 n n C4' H4' GDP sing 192 n n O4' C1' GDP sing 193 n n C3' O3' GDP sing 194 n n C3' C2' GDP sing 195 n n C3' H3' GDP sing 196 n n O3' HO3' GDP sing 197 n n C2' O2' GDP sing 198 n n C2' C1' GDP sing 199 n n C2' H2' GDP sing 200 n n O2' HO2' GDP sing 201 n n C1' N9 GDP sing 202 n n C1' H1' GDP sing 203 n n N9 C8 GDP sing 204 n y N9 C4 GDP sing 205 n y C8 N7 GDP doub 206 n y C8 H8 GDP sing 207 n n N7 C5 GDP sing 208 n y C5 C6 GDP sing 209 n n C5 C4 GDP doub 210 n y C6 O6 GDP doub 211 n n C6 N1 GDP sing 212 n n N1 C2 GDP sing 213 n n N1 HN1 GDP sing 214 n n C2 N2 GDP sing 215 n n C2 N3 GDP doub 216 n n N2 HN21 GDP sing 217 n n N2 HN22 GDP sing 218 n n N3 C4 GDP sing 219 n n # _atom_sites.entry_id 8ZB8 _atom_sites.fract_transf_matrix[1][1] 0.00947 _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] 0.006321 _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] 0.00554 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GOL A 1 504 504 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 503 MES MES . N 11 A1D8I B 1 504 601 A1D8I KKK . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 503 CA CA . R 9 GDP D 1 501 501 GDP GDP . S 11 A1D8I D 1 502 601 A1D8I KKK . T 12 ACP F 1 401 401 ACP ACP . # 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 . . . R 9 25.326 8.763 44.067 1 79.31 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . R 9 25.735 7.769 43.063 1 82.86 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . R 9 24.358 8.244 45.06 1 80.63 -1 O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . R 9 26.424 9.629 44.539 1 82.15 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . R 9 24.512 9.8 43.22 1 75.16 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . R 9 22.95 9.918 43.336 1 71.19 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . R 9 22.41 8.547 43.439 1 72.21 -1 O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . R 9 22.571 10.889 44.36 1 88.63 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . R 9 22.713 10.598 41.948 1 67.44 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . R 9 22.202 11.897 41.879 1 64.42 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . R 9 20.987 11.812 40.993 1 66.93 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . R 9 20.232 10.718 41.409 1 68.89 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . R 9 20.033 12.941 41.163 1 68.17 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . R 9 19.874 13.467 39.872 1 75.44 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . R 9 18.689 12.375 41.458 1 65.04 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . R 9 17.888 12.836 40.406 1 69.65 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . R 9 18.871 10.941 41.172 1 65.45 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . R 9 18.183 9.981 42.024 1 67.78 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . R 9 18.551 9.599 43.234 1 74.69 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . R 9 17.715 8.654 43.698 1 72.27 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . R 9 16.826 8.413 42.753 1 67.24 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . R 9 15.683 7.54 42.594 1 64.05 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . R 9 15.367 6.782 43.501 1 64.56 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . R 9 15.015 7.583 41.463 1 60.69 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . R 9 15.375 8.408 40.495 1 64.66 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . R 9 14.663 8.429 39.369 1 69.51 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . R 9 16.41 9.236 40.566 1 62.38 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . R 9 17.153 9.28 41.655 1 66.32 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #