data_6QVE # _model_server_result.job_id uHanwkC9RhpoRW9JOpPnew _model_server_result.datetime_utc '2025-02-05 18:05:53' _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 6qve # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":501}' # _entry.id 6QVE # _exptl.entry_id 6QVE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 6QVE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QVE _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details software_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 _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 ? 6 J N N ? 6 L 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 OE2 GLU 71 C GLU 71 1_555 G MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc2 F O1G GTP . C GTP 501 1_555 G MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 F O3B GTP . C GTP 501 1_555 G MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc4 F O1B GTP . C GTP 501 1_555 G MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc5 B OE2 GLU 71 A GLU 71 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 H O1G GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc7 H O2G GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc8 H O3B GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc9 H O1B GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 6QVE _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 F 4 GTP C 1 501 501 GTP GTP . G 5 MG C 1 502 502 MG MG . H 4 GTP A 1 501 501 GTP GTP . I 5 MG A 1 502 502 MG MG . J 6 GDP H 1 501 501 GDP GDP . K 7 TA1 H 1 502 601 TA1 TA1 . L 6 GDP G 1 501 501 GDP GDP . M 7 TA1 G 1 502 601 TA1 TA1 . # 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 . . . L 6 179.643 277.404 352.685 1 66.88 ? PB GDP 501 G 1 HETATM 2 O O1B GDP . . . L 6 179.255 277.425 351.212 1 66.88 ? O1B GDP 501 G 1 HETATM 3 O O2B GDP . . . L 6 180.836 278.319 352.872 1 66.88 ? O2B GDP 501 G 1 HETATM 4 O O3B GDP . . . L 6 178.522 277.725 353.587 1 66.88 ? O3B GDP 501 G 1 HETATM 5 O O3A GDP . . . L 6 180.196 275.938 352.961 1 66.88 ? O3A GDP 501 G 1 HETATM 6 P PA GDP . . . L 6 181.283 275.103 352.157 1 66.88 ? PA GDP 501 G 1 HETATM 7 O O1A GDP . . . L 6 181.459 275.808 350.841 1 66.88 ? O1A GDP 501 G 1 HETATM 8 O O2A GDP . . . L 6 182.559 275.11 352.893 1 66.88 ? O2A GDP 501 G 1 HETATM 9 O O5' GDP . . . L 6 180.653 273.68 351.892 1 66.88 ? O5' GDP 501 G 1 HETATM 10 C C5' GDP . . . L 6 181.144 272.432 352.423 1 66.88 ? C5' GDP 501 G 1 HETATM 11 C C4' GDP . . . L 6 181.388 271.49 351.272 1 66.88 ? C4' GDP 501 G 1 HETATM 12 O O4' GDP . . . L 6 182.406 272.039 350.407 1 66.88 ? O4' GDP 501 G 1 HETATM 13 C C3' GDP . . . L 6 181.864 270.091 351.664 1 66.88 ? C3' GDP 501 G 1 HETATM 14 O O3' GDP . . . L 6 181.235 269.091 350.87 1 66.88 ? O3' GDP 501 G 1 HETATM 15 C C2' GDP . . . L 6 183.37 270.159 351.416 1 66.88 ? C2' GDP 501 G 1 HETATM 16 O O2' GDP . . . L 6 183.907 268.891 351.061 1 66.88 ? O2' GDP 501 G 1 HETATM 17 C C1' GDP . . . L 6 183.429 271.087 350.214 1 66.88 ? C1' GDP 501 G 1 HETATM 18 N N9 GDP . . . L 6 184.703 271.796 350.113 1 66.88 ? N9 GDP 501 G 1 HETATM 19 C C8 GDP . . . L 6 185.201 272.731 350.972 1 66.88 ? C8 GDP 501 G 1 HETATM 20 N N7 GDP . . . L 6 186.371 273.189 350.613 1 66.88 ? N7 GDP 501 G 1 HETATM 21 C C5 GDP . . . L 6 186.657 272.51 349.444 1 66.88 ? C5 GDP 501 G 1 HETATM 22 C C6 GDP . . . L 6 187.763 272.591 348.591 1 66.88 ? C6 GDP 501 G 1 HETATM 23 O O6 GDP . . . L 6 188.748 273.309 348.729 1 66.88 ? O6 GDP 501 G 1 HETATM 24 N N1 GDP . . . L 6 187.649 271.755 347.504 1 66.88 ? N1 GDP 501 G 1 HETATM 25 C C2 GDP . . . L 6 186.589 270.932 347.255 1 66.88 ? C2 GDP 501 G 1 HETATM 26 N N2 GDP . . . L 6 186.621 270.218 346.128 1 66.88 ? N2 GDP 501 G 1 HETATM 27 N N3 GDP . . . L 6 185.54 270.838 348.064 1 66.88 ? N3 GDP 501 G 1 HETATM 28 C C4 GDP . . . L 6 185.64 271.649 349.127 1 66.88 ? C4 GDP 501 G 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #