data_7UXH # _model_server_result.job_id BCYpWFcyk01s1VrAf0psJA _model_server_result.datetime_utc '2025-02-05 08:53:37' _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 7uxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":401}' # _entry.id 7UXH # _exptl.entry_id 7UXH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 15 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 7UXH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7UXH _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 36-meric _pdbx_struct_assembly.oligomeric_count 36 _pdbx_struct_assembly.details author_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,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA _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 ? 15 OA N N ? 15 RA N N ? 15 UA N N ? 15 XA 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 F OD2 ASP 62 F ASP 62 1_555 NA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc2 MA O3G GTP . F GTP 401 1_555 NA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc3 MA O2B GTP . F GTP 401 1_555 NA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc4 PA O3G GTP . M GTP 401 1_555 QA MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc5 PA O2B GTP . M GTP 401 1_555 QA MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc6 SA O3G GTP . V GTP 401 1_555 TA MG MG . V MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc7 SA O2B GTP . V GTP 401 1_555 TA MG MG . V MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc8 CA OG1 THR 42 c THR 42 1_555 WA MG MG . c MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc9 VA O3G GTP . c GTP 401 1_555 WA MG MG . c MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc10 VA O2B GTP . c GTP 401 1_555 WA MG MG . c MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _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 7UXH _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 KA 12 IHP A 1 2601 2601 IHP IHP . LA 12 IHP C 1 2601 2601 IHP IHP . MA 13 GTP F 1 401 401 GTP GTP . NA 14 MG F 1 402 402 MG MG . OA 15 GDP G 1 401 401 GDP GDP . PA 13 GTP M 1 401 401 GTP GTP . QA 14 MG M 1 402 402 MG MG . RA 15 GDP N 1 401 401 GDP GDP . SA 13 GTP V 1 401 401 GTP GTP . TA 14 MG V 1 402 402 MG MG . UA 15 GDP W 1 401 401 GDP GDP . VA 13 GTP c 1 401 401 GTP GTP . WA 14 MG c 1 402 402 MG MG . XA 15 GDP d 1 401 401 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 . . . OA 15 260.711 172.705 272.299 1 76.03 ? PB GDP 401 G 1 HETATM 2 O O1B GDP . . . OA 15 259.806 173.041 271.139 1 76.03 ? O1B GDP 401 G 1 HETATM 3 O O2B GDP . . . OA 15 259.981 171.825 273.281 1 76.03 ? O2B GDP 401 G 1 HETATM 4 O O3B GDP . . . OA 15 261.941 171.995 271.793 1 76.03 ? O3B GDP 401 G 1 HETATM 5 O O3A GDP . . . OA 15 261.14 174.057 273.049 1 76.03 ? O3A GDP 401 G 1 HETATM 6 P PA GDP . . . OA 15 262.501 174.813 272.657 1 76.03 ? PA GDP 401 G 1 HETATM 7 O O1A GDP . . . OA 15 262.672 174.861 271.159 1 76.03 ? O1A GDP 401 G 1 HETATM 8 O O2A GDP . . . OA 15 263.698 174.176 273.317 1 76.03 ? O2A GDP 401 G 1 HETATM 9 O O5' GDP . . . OA 15 262.233 176.281 273.242 1 76.03 ? O5' GDP 401 G 1 HETATM 10 C C5' GDP . . . OA 15 263.275 177.237 273.383 1 76.03 ? C5' GDP 401 G 1 HETATM 11 C C4' GDP . . . OA 15 262.598 178.507 273.867 1 76.03 ? C4' GDP 401 G 1 HETATM 12 O O4' GDP . . . OA 15 262.314 178.43 275.268 1 76.03 ? O4' GDP 401 G 1 HETATM 13 C C3' GDP . . . OA 15 263.484 179.723 273.678 1 76.03 ? C3' GDP 401 G 1 HETATM 14 O O3' GDP . . . OA 15 262.647 180.855 273.401 1 76.03 ? O3' GDP 401 G 1 HETATM 15 C C2' GDP . . . OA 15 264.224 179.785 275 1 76.03 ? C2' GDP 401 G 1 HETATM 16 O O2' GDP . . . OA 15 264.721 181.086 275.331 1 76.03 ? O2' GDP 401 G 1 HETATM 17 C C1' GDP . . . OA 15 263.172 179.32 275.991 1 76.03 ? C1' GDP 401 G 1 HETATM 18 N N9 GDP . . . OA 15 263.808 178.678 277.166 1 76.03 ? N9 GDP 401 G 1 HETATM 19 C C8 GDP . . . OA 15 264.343 177.447 277.23 1 76.03 ? C8 GDP 401 G 1 HETATM 20 N N7 GDP . . . OA 15 264.83 177.201 278.474 1 76.03 ? N7 GDP 401 G 1 HETATM 21 C C5 GDP . . . OA 15 264.596 178.29 279.226 1 76.03 ? C5 GDP 401 G 1 HETATM 22 C C6 GDP . . . OA 15 264.842 178.708 280.622 1 76.03 ? C6 GDP 401 G 1 HETATM 23 O O6 GDP . . . OA 15 265.413 177.944 281.425 1 76.03 ? O6 GDP 401 G 1 HETATM 24 N N1 GDP . . . OA 15 264.438 179.927 280.998 1 76.03 ? N1 GDP 401 G 1 HETATM 25 C C2 GDP . . . OA 15 263.821 180.77 280.154 1 76.03 ? C2 GDP 401 G 1 HETATM 26 N N2 GDP . . . OA 15 263.44 181.99 280.603 1 76.03 ? N2 GDP 401 G 1 HETATM 27 N N3 GDP . . . OA 15 263.565 180.454 278.863 1 76.03 ? N3 GDP 401 G 1 HETATM 28 C C4 GDP . . . OA 15 263.921 179.254 278.357 1 76.03 ? C4 GDP 401 G 1 HETATM 29 H H4' GDP . . . OA 15 261.676 178.649 273.292 1 76.03 ? H4' GDP 401 G 1 HETATM 30 H H3' GDP . . . OA 15 264.194 179.544 272.858 1 76.03 ? H3' GDP 401 G 1 HETATM 31 H HO3' GDP . . . OA 15 262.911 181.63 273.91 1 76.03 ? HO3' GDP 401 G 1 HETATM 32 H H2' GDP . . . OA 15 265.048 179.059 274.98 1 76.03 ? H2' GDP 401 G 1 HETATM 33 H HO2' GDP . . . OA 15 265.544 180.996 275.829 1 76.03 ? HO2' GDP 401 G 1 HETATM 34 H H1' GDP . . . OA 15 262.596 180.196 276.32 1 76.03 ? H1' GDP 401 G 1 HETATM 35 H H8 GDP . . . OA 15 264.387 176.756 276.399 1 76.03 ? H8 GDP 401 G 1 HETATM 36 H HN1 GDP . . . OA 15 264.603 180.236 281.973 1 76.03 ? HN1 GDP 401 G 1 HETATM 37 H HN21 GDP . . . OA 15 263.617 182.26 281.56 1 76.03 ? HN21 GDP 401 G 1 HETATM 38 H HN22 GDP . . . OA 15 262.977 182.633 279.977 1 76.03 ? HN22 GDP 401 G 1 # _model_server_stats.io_time_ms 183 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 458 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 38 #