data_8YU9 # _model_server_result.job_id wAfPbId1oZ0qI-8ry661aA _model_server_result.datetime_utc '2024-10-18 06:24:25' _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 8yu9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":502}' # _entry.id 8YU9 # _exptl.entry_id 8YU9 _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 8YU9 _cell.length_a 104.974 _cell.length_b 157.379 _cell.length_c 182.635 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YU9 _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 S 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 covale ? covale1 B NH2 ARG 251 B ARG 251 1_555 L O3S MES . B MES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 A OD2 ASP 39 A ASP 39 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc2 A OG1 THR 41 A THR 41 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 A O GLY 44 A GLY 44 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc4 A OD2 ASP 47 A ASP 47 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A OD1 ASN 50 A ASN 50 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc7 A OE2 GLU 71 A GLU 71 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc11 B OD2 ASP 177 B ASP 177 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc12 K O2A GDP . B GDP 502 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc15 C OG1 THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc16 C OD2 ASP 47 C ASP 47 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc18 O O3G GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc19 O O2B GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? # _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 171 n n PB O2B GDP sing 172 n n PB O3B GDP sing 173 n n PB O3A GDP sing 174 n n O2B HOB2 GDP sing 175 n n O3B HOB3 GDP sing 176 n n O3A PA GDP sing 177 n n PA O1A GDP doub 178 n n PA O2A GDP sing 179 n n PA O5' GDP sing 180 n n O2A HOA2 GDP sing 181 n n O5' C5' GDP sing 182 n n C5' C4' GDP sing 183 n n C5' H5' GDP sing 184 n n C5' "H5''" GDP sing 185 n n C4' O4' GDP sing 186 n n C4' C3' GDP sing 187 n n C4' H4' GDP sing 188 n n O4' C1' GDP sing 189 n n C3' O3' GDP sing 190 n n C3' C2' GDP sing 191 n n C3' H3' GDP sing 192 n n O3' HO3' GDP sing 193 n n C2' O2' GDP sing 194 n n C2' C1' GDP sing 195 n n C2' H2' GDP sing 196 n n O2' HO2' GDP sing 197 n n C1' N9 GDP sing 198 n n C1' H1' GDP sing 199 n n N9 C8 GDP sing 200 n y N9 C4 GDP sing 201 n y C8 N7 GDP doub 202 n y C8 H8 GDP sing 203 n n N7 C5 GDP sing 204 n y C5 C6 GDP sing 205 n n C5 C4 GDP doub 206 n y C6 O6 GDP doub 207 n n C6 N1 GDP sing 208 n n N1 C2 GDP sing 209 n n N1 HN1 GDP sing 210 n n C2 N2 GDP sing 211 n n C2 N3 GDP doub 212 n n N2 HN21 GDP sing 213 n n N2 HN22 GDP sing 214 n n N3 C4 GDP sing 215 n n # _atom_sites.entry_id 8YU9 _atom_sites.fract_transf_matrix[1][1] 0.009526 _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] 0.006354 _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] 0.005475 _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 CA A 1 502 502 CA CA . I 7 MG A 1 503 503 MG MG . J 8 A1D7A B 1 501 505 A1D7A LIG . K 9 GDP B 1 502 501 GDP GDP . L 10 MES B 1 503 502 MES MES . M 10 MES B 1 504 503 MES MES . N 7 MG B 1 505 504 MG MG . O 5 GTP C 1 501 501 GTP GTP . P 6 CA C 1 502 502 CA CA . Q 7 MG C 1 503 503 MG MG . R 8 A1D7A D 1 501 502 A1D7A LIG . S 9 GDP D 1 502 501 GDP GDP . T 11 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 . . . K 9 18.774 -49.596 -15.762 0 58.51 ? PB GDP 502 B 1 HETATM 2 O O1B GDP . . . K 9 18.914 -50.707 -16.776 0 57.56 ? O1B GDP 502 B 1 HETATM 3 O O2B GDP . . . K 9 18.366 -50.159 -14.422 0 60.58 ? O2B GDP 502 B 1 HETATM 4 O O3B GDP . . . K 9 20.102 -48.893 -15.607 0 58.93 ? O3B GDP 502 B 1 HETATM 5 O O3A GDP . . . K 9 17.674 -48.528 -16.256 0 58.23 ? O3A GDP 502 B 1 HETATM 6 P PA GDP . . . K 9 16.346 -48.997 -17.037 0 58.83 ? PA GDP 502 B 1 HETATM 7 O O1A GDP . . . K 9 16.597 -50.265 -17.816 0 58.1 ? O1A GDP 502 B 1 HETATM 8 O O2A GDP . . . K 9 15.204 -49.191 -16.067 0 60.43 ? O2A GDP 502 B 1 HETATM 9 O O5' GDP . . . K 9 16.028 -47.774 -18.034 0 58 ? O5' GDP 502 B 1 HETATM 10 C C5' GDP . . . K 9 14.732 -47.179 -18.043 0 57.62 ? C5' GDP 502 B 1 HETATM 11 C C4' GDP . . . K 9 14.159 -47.188 -19.453 0 57.56 ? C4' GDP 502 B 1 HETATM 12 O O4' GDP . . . K 9 13.931 -48.546 -19.834 0 57.84 ? O4' GDP 502 B 1 HETATM 13 C C3' GDP . . . K 9 12.823 -46.465 -19.5 0 57.21 ? C3' GDP 502 B 1 HETATM 14 O O3' GDP . . . K 9 12.87 -45.406 -20.461 0 57.33 ? O3' GDP 502 B 1 HETATM 15 C C2' GDP . . . K 9 11.796 -47.498 -19.916 0 57.53 ? C2' GDP 502 B 1 HETATM 16 O O2' GDP . . . K 9 11.075 -47.044 -21.065 0 58.6 ? O2' GDP 502 B 1 HETATM 17 C C1' GDP . . . K 9 12.58 -48.758 -20.247 0 57.24 ? C1' GDP 502 B 1 HETATM 18 N N9 GDP . . . K 9 12.021 -49.917 -19.508 0 57.1 ? N9 GDP 502 B 1 HETATM 19 C C8 GDP . . . K 9 12.271 -50.212 -18.218 0 57.56 ? C8 GDP 502 B 1 HETATM 20 N N7 GDP . . . K 9 11.614 -51.336 -17.835 0 57.77 ? N7 GDP 502 B 1 HETATM 21 C C5 GDP . . . K 9 10.925 -51.782 -18.901 0 57.02 ? C5 GDP 502 B 1 HETATM 22 C C6 GDP . . . K 9 10.023 -52.923 -19.187 0 57.69 ? C6 GDP 502 B 1 HETATM 23 O O6 GDP . . . K 9 9.745 -53.761 -18.302 0 59.59 ? O6 GDP 502 B 1 HETATM 24 N N1 GDP . . . K 9 9.515 -53.027 -20.421 0 57.6 ? N1 GDP 502 B 1 HETATM 25 C C2 GDP . . . K 9 9.797 -52.139 -21.394 0 56.42 ? C2 GDP 502 B 1 HETATM 26 N N2 GDP . . . K 9 9.241 -52.319 -22.616 0 56.81 ? N2 GDP 502 B 1 HETATM 27 N N3 GDP . . . K 9 10.615 -51.072 -21.203 0 56.07 ? N3 GDP 502 B 1 HETATM 28 C C4 GDP . . . K 9 11.197 -50.845 -20.001 0 56.37 ? C4 GDP 502 B 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #