data_2P8Y # _model_server_result.job_id IPE0QityxFVGw6TsC2-tIw _model_server_result.datetime_utc '2025-01-02 17:02:39' _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 2p8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":843}' # _entry.id 2P8Y # _exptl.entry_id 2P8Y _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 2P8Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 ILE 698 T ILE 698 1_555 A N DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.891 ? covale ? covale2 A O ILE 698 T ILE 698 1_555 A N DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.743 ? covale ? covale3 A C ILE 698 T ILE 698 1_555 A CA DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? covale ? covale4 A CA ILE 698 T ILE 698 1_555 A N DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale5 A O DDE 699 T DDE 699 1_555 A N ARG 700 T ARG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale6 A NE2 DDE 699 T DDE 699 1_555 B C1D APR . T APR 1699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? # _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 190 n n PB O2B GDP sing 191 n n PB O3B GDP sing 192 n n PB O3A GDP sing 193 n n O2B HOB2 GDP sing 194 n n O3B HOB3 GDP sing 195 n n O3A PA GDP sing 196 n n PA O1A GDP doub 197 n n PA O2A GDP sing 198 n n PA O5' GDP sing 199 n n O2A HOA2 GDP sing 200 n n O5' C5' GDP sing 201 n n C5' C4' GDP sing 202 n n C5' H5' GDP sing 203 n n C5' "H5''" GDP sing 204 n n C4' O4' GDP sing 205 n n C4' C3' GDP sing 206 n n C4' H4' GDP sing 207 n n O4' C1' GDP sing 208 n n C3' O3' GDP sing 209 n n C3' C2' GDP sing 210 n n C3' H3' GDP sing 211 n n O3' HO3' GDP sing 212 n n C2' O2' GDP sing 213 n n C2' C1' GDP sing 214 n n C2' H2' GDP sing 215 n n O2' HO2' GDP sing 216 n n C1' N9 GDP sing 217 n n C1' H1' GDP sing 218 n n N9 C8 GDP sing 219 n y N9 C4 GDP sing 220 n y C8 N7 GDP doub 221 n y C8 H8 GDP sing 222 n n N7 C5 GDP sing 223 n y C5 C6 GDP sing 224 n n C5 C4 GDP doub 225 n y C6 O6 GDP doub 226 n n C6 N1 GDP sing 227 n n N1 C2 GDP sing 228 n n N1 HN1 GDP sing 229 n n C2 N2 GDP sing 230 n n C2 N3 GDP doub 231 n n N2 HN21 GDP sing 232 n n N2 HN22 GDP sing 233 n n N3 C4 GDP sing 234 n n # _atom_sites.entry_id 2P8Y _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 B 2 APR T 1 1699 1699 APR APR . C 3 SO1 T 1 1700 800 SO1 SO1 . D 4 GDP T 1 843 843 GDP GDP . # 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 . . . D 4 -15.279 49.567 -64.264 1 50.17 ? PB GDP 843 T 1 HETATM 2 O O1B GDP . . . D 4 -16.149 48.76 -65.154 1 49.03 ? O1B GDP 843 T 1 HETATM 3 O O2B GDP . . . D 4 -14.937 48.882 -62.951 1 52.66 ? O2B GDP 843 T 1 HETATM 4 O O3B GDP . . . D 4 -15.831 50.983 -64.018 1 50.82 ? O3B GDP 843 T 1 HETATM 5 O O3A GDP . . . D 4 -13.839 49.78 -65.073 1 52.02 ? O3A GDP 843 T 1 HETATM 6 P PA GDP . . . D 4 -12.56 50.607 -64.688 1 52.42 ? PA GDP 843 T 1 HETATM 7 O O1A GDP . . . D 4 -12.302 50.588 -63.232 1 55.6 ? O1A GDP 843 T 1 HETATM 8 O O2A GDP . . . D 4 -12.62 51.993 -65.294 1 53.38 ? O2A GDP 843 T 1 HETATM 9 O O5' GDP . . . D 4 -11.418 49.814 -65.464 1 51.14 ? O5' GDP 843 T 1 HETATM 10 C C5' GDP . . . D 4 -11.109 48.456 -65.128 1 49.92 ? C5' GDP 843 T 1 HETATM 11 C C4' GDP . . . D 4 -9.733 48.141 -65.656 1 48.74 ? C4' GDP 843 T 1 HETATM 12 O O4' GDP . . . D 4 -9.775 48.291 -67.114 1 48.39 ? O4' GDP 843 T 1 HETATM 13 C C3' GDP . . . D 4 -8.62 49.071 -65.117 1 48.64 ? C3' GDP 843 T 1 HETATM 14 O O3' GDP . . . D 4 -7.449 48.189 -64.944 1 47.17 ? O3' GDP 843 T 1 HETATM 15 C C2' GDP . . . D 4 -8.417 50.064 -66.247 1 47.07 ? C2' GDP 843 T 1 HETATM 16 O O2' GDP . . . D 4 -7.148 50.657 -66.224 1 46.29 ? O2' GDP 843 T 1 HETATM 17 C C1' GDP . . . D 4 -8.791 49.226 -67.492 1 47.76 ? C1' GDP 843 T 1 HETATM 18 N N9 GDP . . . D 4 -9.352 50.138 -68.66 1 49.03 ? N9 GDP 843 T 1 HETATM 19 C C8 GDP . . . D 4 -10.338 51.092 -68.566 1 48.46 ? C8 GDP 843 T 1 HETATM 20 N N7 GDP . . . D 4 -10.546 51.669 -69.762 1 46.91 ? N7 GDP 843 T 1 HETATM 21 C C5 GDP . . . D 4 -9.652 51.044 -70.635 1 48.48 ? C5 GDP 843 T 1 HETATM 22 C C6 GDP . . . D 4 -9.406 51.245 -72.03 1 47.82 ? C6 GDP 843 T 1 HETATM 23 O O6 GDP . . . D 4 -9.986 52.053 -72.772 1 46.89 ? O6 GDP 843 T 1 HETATM 24 N N1 GDP . . . D 4 -8.396 50.401 -72.552 1 49.47 ? N1 GDP 843 T 1 HETATM 25 C C2 GDP . . . D 4 -7.705 49.472 -71.78 1 49.95 ? C2 GDP 843 T 1 HETATM 26 N N2 GDP . . . D 4 -6.762 48.724 -72.382 1 49.31 ? N2 GDP 843 T 1 HETATM 27 N N3 GDP . . . D 4 -7.938 49.288 -70.467 1 49.33 ? N3 GDP 843 T 1 HETATM 28 C C4 GDP . . . D 4 -8.908 50.106 -69.965 1 49.29 ? C4 GDP 843 T 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #