data_6HZ5 # _model_server_result.job_id P1wmpeyU8crb0KjMwU3QoQ _model_server_result.datetime_utc '2025-03-06 08:53:16' _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 6hz5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1001}' # _entry.id 6HZ5 # _exptl.entry_id 6HZ5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 6HZ5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HZ5 _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 tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 ? _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 ? 5 U N N ? 5 V N N ? 5 W N N ? 5 DA N N ? 5 EA N N ? 5 FA 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 OG1 THR 47 A THR 208 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc2 A OD2 ASP 118 A ASP 279 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc3 O O3G GNP . A GNP 1001 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc4 O O1B GNP . A GNP 1001 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc5 B OG1 THR 47 B THR 208 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc6 Q O3G GNP . B GNP 1001 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc7 Q O2B GNP . B GNP 1001 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc8 C OG1 THR 47 C THR 208 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc9 S O3G GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc10 S O2B GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc11 S O2A GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc12 H OG1 THR 47 G THR 208 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc13 H OD2 ASP 118 G ASP 279 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc14 X O3G GNP . G GNP 1001 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc15 X O1B GNP . G GNP 1001 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc16 I OG1 THR 47 H THR 208 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc17 Z O3G GNP . H GNP 1001 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc18 Z O2B GNP . H GNP 1001 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc19 J OG1 THR 47 I THR 208 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc20 BA O3G GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc21 BA O2B GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc22 BA O2A GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? # _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 6HZ5 _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 O 3 GNP A 1 1001 1001 GNP GNP . P 4 MG A 1 1002 1002 MG MG . Q 3 GNP B 1 1001 1001 GNP GNP . R 4 MG B 1 1002 1002 MG MG . S 3 GNP C 1 1001 1001 GNP GNP . T 4 MG C 1 1002 1002 MG MG . U 5 GDP D 1 1001 1001 GDP GDP . V 5 GDP E 1 1001 1001 GDP GDP . W 5 GDP F 1 1001 1001 GDP GDP . X 3 GNP G 1 1001 1001 GNP GNP . Y 4 MG G 1 1002 1002 MG MG . Z 3 GNP H 1 1001 1001 GNP GNP . AA 4 MG H 1 1002 1002 MG MG . BA 3 GNP I 1 1001 1001 GNP GNP . CA 4 MG I 1 1002 1002 MG MG . DA 5 GDP J 1 1001 1001 GDP GDP . EA 5 GDP K 1 1001 1001 GDP GDP . FA 5 GDP L 1 1001 1001 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 . . . W 5 105.107 89.521 133.862 1 134.89 ? PB GDP 1001 F 1 HETATM 2 O O1B GDP . . . W 5 105.462 89.539 132.429 1 134.89 ? O1B GDP 1001 F 1 HETATM 3 O O2B GDP . . . W 5 105.745 90.677 134.527 1 134.89 ? O2B GDP 1001 F 1 HETATM 4 O O3B GDP . . . W 5 103.64 89.615 134.021 1 134.89 ? O3B GDP 1001 F 1 HETATM 5 O O3A GDP . . . W 5 105.61 88.142 134.502 1 134.89 ? O3A GDP 1001 F 1 HETATM 6 P PA GDP . . . W 5 106.141 88.087 136.01 1 134.89 ? PA GDP 1001 F 1 HETATM 7 O O1A GDP . . . W 5 107.035 89.234 136.284 1 134.89 ? O1A GDP 1001 F 1 HETATM 8 O O2A GDP . . . W 5 104.978 88.115 136.914 1 134.89 ? O2A GDP 1001 F 1 HETATM 9 O O5' GDP . . . W 5 106.969 86.73 136.234 1 134.89 ? O5' GDP 1001 F 1 HETATM 10 C C5' GDP . . . W 5 107.274 85.922 135.103 1 134.89 ? C5' GDP 1001 F 1 HETATM 11 C C4' GDP . . . W 5 107.954 84.584 135.468 1 134.89 ? C4' GDP 1001 F 1 HETATM 12 O O4' GDP . . . W 5 109.302 84.894 135.994 1 134.89 ? O4' GDP 1001 F 1 HETATM 13 C C3' GDP . . . W 5 107.256 83.828 136.605 1 134.89 ? C3' GDP 1001 F 1 HETATM 14 O O3' GDP . . . W 5 107.438 82.413 136.432 1 134.89 ? O3' GDP 1001 F 1 HETATM 15 C C2' GDP . . . W 5 108.062 84.307 137.786 1 134.89 ? C2' GDP 1001 F 1 HETATM 16 O O2' GDP . . . W 5 107.857 83.468 138.929 1 134.89 ? O2' GDP 1001 F 1 HETATM 17 C C1' GDP . . . W 5 109.445 84.126 137.217 1 134.89 ? C1' GDP 1001 F 1 HETATM 18 N N9 GDP . . . W 5 110.464 84.686 138.113 1 134.89 ? N9 GDP 1001 F 1 HETATM 19 C C8 GDP . . . W 5 110.686 85.992 138.122 1 134.89 ? C8 GDP 1001 F 1 HETATM 20 N N7 GDP . . . W 5 111.638 86.242 139.009 1 134.89 ? N7 GDP 1001 F 1 HETATM 21 C C5 GDP . . . W 5 111.995 85.088 139.558 1 134.89 ? C5 GDP 1001 F 1 HETATM 22 C C6 GDP . . . W 5 112.901 84.821 140.489 1 134.89 ? C6 GDP 1001 F 1 HETATM 23 O O6 GDP . . . W 5 113.56 85.723 140.994 1 134.89 ? O6 GDP 1001 F 1 HETATM 24 N N1 GDP . . . W 5 113.094 83.51 140.907 1 134.89 ? N1 GDP 1001 F 1 HETATM 25 C C2 GDP . . . W 5 112.323 82.508 140.322 1 134.89 ? C2 GDP 1001 F 1 HETATM 26 N N2 GDP . . . W 5 112.48 81.242 140.697 1 134.89 ? N2 GDP 1001 F 1 HETATM 27 N N3 GDP . . . W 5 111.422 82.839 139.387 1 134.89 ? N3 GDP 1001 F 1 HETATM 28 C C4 GDP . . . W 5 111.269 84.116 139.005 1 134.89 ? C4 GDP 1001 F 1 HETATM 29 H H5' GDP . . . W 5 107.926 86.495 134.459 1 134.89 ? H5' GDP 1001 F 1 HETATM 30 H "H5''" GDP . . . W 5 106.344 85.713 134.575 1 134.89 ? "H5''" GDP 1001 F 1 HETATM 31 H H4' GDP . . . W 5 107.951 83.959 134.577 1 134.89 ? H4' GDP 1001 F 1 HETATM 32 H H3' GDP . . . W 5 106.19 84.044 136.676 1 134.89 ? H3' GDP 1001 F 1 HETATM 33 H HO3' GDP . . . W 5 106.974 82.117 135.597 1 134.89 ? HO3' GDP 1001 F 1 HETATM 34 H H2' GDP . . . W 5 107.883 85.356 137.975 1 134.89 ? H2' GDP 1001 F 1 HETATM 35 H HO2' GDP . . . W 5 108.05 82.518 138.687 1 134.89 ? HO2' GDP 1001 F 1 HETATM 36 H H1' GDP . . . W 5 109.653 83.083 136.992 1 134.89 ? H1' GDP 1001 F 1 HETATM 37 H H8 GDP . . . W 5 110.183 86.726 137.497 1 134.89 ? H8 GDP 1001 F 1 HETATM 38 H HN1 GDP . . . W 5 113.771 83.296 141.611 1 134.89 ? HN1 GDP 1001 F 1 HETATM 39 H HN21 GDP . . . W 5 113.154 81.009 141.399 1 134.89 ? HN21 GDP 1001 F 1 HETATM 40 H HN22 GDP . . . W 5 111.925 80.525 140.276 1 134.89 ? HN22 GDP 1001 F 1 # _model_server_stats.io_time_ms 380 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #