data_3QE0 # _model_server_result.job_id GTNm9x6_WHAxXY32oxAv2Q _model_server_result.datetime_utc '2025-03-21 15:56:25' _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 3qe0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":355}' # _entry.id 3QE0 # _exptl.entry_id 3QE0 _exptl.method 'X-RAY DIFFRACTION' # _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 3 _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 120 _cell.entry_id 3QE0 _cell.length_a 106.637 _cell.length_b 106.637 _cell.length_c 455.062 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QE0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,L 1 1 B,D,H,I,M 2 1 C,J,K,N 3 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 ? 4 G N N ? 4 I N N ? 4 K 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 OG SER 18 A SER 47 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc2 A OG1 THR 152 A THR 181 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc3 G O1B GDP . A GDP 555 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc4 B OG SER 18 B SER 47 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc5 I O1B GDP . B GDP 355 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc6 I O2B GDP . B GDP 355 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc7 C OG SER 18 C SER 47 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc8 C OG1 THR 152 C THR 181 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc9 K O1B GDP . C GDP 551 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc10 K O2B GDP . C GDP 551 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? # _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 3QE0 _atom_sites.fract_transf_matrix[1][1] 0.009378 _atom_sites.fract_transf_matrix[1][2] 0.005414 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010828 _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] 0.002198 _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 3 MG A 1 556 556 MG MG . G 4 GDP A 1 555 555 GDP GDP . H 3 MG B 1 556 556 MG MG . I 4 GDP B 1 355 355 GDP GDP . J 3 MG C 1 552 552 MG MG . K 4 GDP C 1 551 551 GDP GDP . L 5 HOH A 1 1 1 HOH HOH . L 5 HOH A 2 2 2 HOH HOH . L 5 HOH A 3 6 6 HOH HOH . L 5 HOH A 4 7 7 HOH HOH . L 5 HOH A 5 8 8 HOH HOH . L 5 HOH A 6 9 9 HOH HOH . L 5 HOH A 7 11 11 HOH HOH . M 5 HOH B 1 3 3 HOH HOH . M 5 HOH B 2 4 4 HOH HOH . M 5 HOH B 3 10 10 HOH HOH . M 5 HOH B 4 12 12 HOH HOH . N 5 HOH C 1 5 5 HOH HOH . # 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 . . . I 4 21.851 -33.792 18.638 1 61.16 ? PB GDP 355 B 1 HETATM 2 O O1B GDP . . . I 4 22.632 -34.631 17.665 1 64.74 ? O1B GDP 355 B 1 HETATM 3 O O2B GDP . . . I 4 20.661 -33.185 17.934 1 61.56 ? O2B GDP 355 B 1 HETATM 4 O O3B GDP . . . I 4 21.393 -34.648 19.783 1 61.71 ? O3B GDP 355 B 1 HETATM 5 O O3A GDP . . . I 4 22.778 -32.605 19.196 1 56.97 ? O3A GDP 355 B 1 HETATM 6 P PA GDP . . . I 4 24.233 -32.819 19.861 1 53.63 ? PA GDP 355 B 1 HETATM 7 O O1A GDP . . . I 4 25.289 -32.248 18.942 1 59.44 ? O1A GDP 355 B 1 HETATM 8 O O2A GDP . . . I 4 24.563 -34.243 20.217 1 52.43 ? O2A GDP 355 B 1 HETATM 9 O O5' GDP . . . I 4 24.092 -31.906 21.175 1 46.79 ? O5' GDP 355 B 1 HETATM 10 C C5' GDP . . . I 4 24.408 -32.429 22.45 1 43.3 ? C5' GDP 355 B 1 HETATM 11 C C4' GDP . . . I 4 25.197 -31.388 23.218 1 43.8 ? C4' GDP 355 B 1 HETATM 12 O O4' GDP . . . I 4 25.419 -31.943 24.504 1 43.25 ? O4' GDP 355 B 1 HETATM 13 C C3' GDP . . . I 4 26.565 -31.174 22.603 1 46.02 ? C3' GDP 355 B 1 HETATM 14 O O3' GDP . . . I 4 27.012 -29.843 22.872 1 50.55 ? O3' GDP 355 B 1 HETATM 15 C C2' GDP . . . I 4 27.463 -32.157 23.315 1 45.36 ? C2' GDP 355 B 1 HETATM 16 O O2' GDP . . . I 4 28.737 -31.569 23.558 1 45.08 ? O2' GDP 355 B 1 HETATM 17 C C1' GDP . . . I 4 26.758 -32.414 24.631 1 41.42 ? C1' GDP 355 B 1 HETATM 18 N N9 GDP . . . I 4 26.657 -33.852 24.951 1 39.49 ? N9 GDP 355 B 1 HETATM 19 C C8 GDP . . . I 4 26.141 -34.822 24.171 1 41.99 ? C8 GDP 355 B 1 HETATM 20 N N7 GDP . . . I 4 26.188 -36.024 24.803 1 42.74 ? N7 GDP 355 B 1 HETATM 21 C C5 GDP . . . I 4 26.725 -35.818 26.019 1 40.2 ? C5 GDP 355 B 1 HETATM 22 C C6 GDP . . . I 4 27.058 -36.646 27.196 1 43.49 ? C6 GDP 355 B 1 HETATM 23 O O6 GDP . . . I 4 26.834 -37.872 27.197 1 49.98 ? O6 GDP 355 B 1 HETATM 24 N N1 GDP . . . I 4 27.607 -36.038 28.255 1 41.26 ? N1 GDP 355 B 1 HETATM 25 C C2 GDP . . . I 4 27.861 -34.714 28.28 1 37.03 ? C2 GDP 355 B 1 HETATM 26 N N2 GDP . . . I 4 28.419 -34.177 29.391 1 33.89 ? N2 GDP 355 B 1 HETATM 27 N N3 GDP . . . I 4 27.584 -33.891 27.239 1 37.71 ? N3 GDP 355 B 1 HETATM 28 C C4 GDP . . . I 4 27.026 -34.384 26.111 1 37.36 ? C4 GDP 355 B 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 28 #