data_8JPC # _model_server_result.job_id rNP0qg6qexpcDhskQRQIdA _model_server_result.datetime_utc '2024-11-13 15:49:56' _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 8jpc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 8JPC # _exptl.entry_id 8JPC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 8JPC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JPC _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I _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 7 _struct_asym.id G _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 disulf ? disulf1 B SG CYS 141 R CYS 141 1_555 B SG CYS 224 R CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc1 D OG SER 47 Q SER 53 1_555 H MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc2 D OG1 THR 180 Q THR 186 1_555 H MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc3 G O3B GDP . Q GDP 401 1_555 H MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 8JPC _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 E 5 SRW R 1 501 401 SRW LIG . F 6 STU G 1 701 701 STU STU . G 7 GDP Q 1 401 360 GDP GDP . H 8 MG Q 1 402 361 MG MG . I 9 ALF Q 1 403 362 ALF ALF . # 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 7 109.822 140.417 57.31 1 99.45 ? PB GDP 401 Q 1 HETATM 2 O O1B GDP . . . G 7 110.173 138.958 57.439 1 99.45 -1 O1B GDP 401 Q 1 HETATM 3 O O2B GDP . . . G 7 111.051 141.255 57.556 1 99.45 ? O2B GDP 401 Q 1 HETATM 4 O O3B GDP . . . G 7 108.755 140.788 58.311 1 99.45 ? O3B GDP 401 Q 1 HETATM 5 O O3A GDP . . . G 7 109.298 140.706 55.823 1 99.45 ? O3A GDP 401 Q 1 HETATM 6 P PA GDP . . . G 7 108.724 142.161 55.47 1 99.45 ? PA GDP 401 Q 1 HETATM 7 O O1A GDP . . . G 7 107.218 142.141 55.502 1 99.45 -1 O1A GDP 401 Q 1 HETATM 8 O O2A GDP . . . G 7 109.277 143.187 56.428 1 99.45 ? O2A GDP 401 Q 1 HETATM 9 O O5' GDP . . . G 7 109.238 142.444 53.976 1 99.45 ? O5' GDP 401 Q 1 HETATM 10 C C5' GDP . . . G 7 109.745 143.736 53.664 1 99.45 ? C5' GDP 401 Q 1 HETATM 11 C C4' GDP . . . G 7 109.252 144.167 52.294 1 99.45 ? C4' GDP 401 Q 1 HETATM 12 O O4' GDP . . . G 7 109.622 143.201 51.312 1 99.45 ? O4' GDP 401 Q 1 HETATM 13 C C3' GDP . . . G 7 107.737 144.262 52.265 1 99.45 ? C3' GDP 401 Q 1 HETATM 14 O O3' GDP . . . G 7 107.344 145.622 52.075 1 99.45 ? O3' GDP 401 Q 1 HETATM 15 C C2' GDP . . . G 7 107.292 143.429 51.081 1 99.45 ? C2' GDP 401 Q 1 HETATM 16 O O2' GDP . . . G 7 106.439 144.197 50.23 1 99.45 ? O2' GDP 401 Q 1 HETATM 17 C C1' GDP . . . G 7 108.573 143.07 50.354 1 99.45 ? C1' GDP 401 Q 1 HETATM 18 N N9 GDP . . . G 7 108.52 141.685 49.835 1 99.45 ? N9 GDP 401 Q 1 HETATM 19 C C8 GDP . . . G 7 108.463 140.562 50.57 1 99.45 ? C8 GDP 401 Q 1 HETATM 20 N N7 GDP . . . G 7 108.433 139.462 49.776 1 99.45 ? N7 GDP 401 Q 1 HETATM 21 C C5 GDP . . . G 7 108.48 139.884 48.501 1 99.45 ? C5 GDP 401 Q 1 HETATM 22 C C6 GDP . . . G 7 108.484 139.25 47.165 1 99.45 ? C6 GDP 401 Q 1 HETATM 23 O O6 GDP . . . G 7 108.437 138.007 47.046 1 99.45 ? O6 GDP 401 Q 1 HETATM 24 N N1 GDP . . . G 7 108.542 140.044 46.092 1 99.45 ? N1 GDP 401 Q 1 HETATM 25 C C2 GDP . . . G 7 108.596 141.384 46.192 1 99.45 ? C2 GDP 401 Q 1 HETATM 26 N N2 GDP . . . G 7 108.651 142.118 45.056 1 99.45 ? N2 GDP 401 Q 1 HETATM 27 N N3 GDP . . . G 7 108.595 142.033 47.382 1 99.45 ? N3 GDP 401 Q 1 HETATM 28 C C4 GDP . . . G 7 108.54 141.348 48.546 1 99.45 ? C4 GDP 401 Q 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #