data_2XTO # _model_server_result.job_id WoBDdu3Qf1FNofdYpzGs6w _model_server_result.datetime_utc '2025-03-04 07:41:56' _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 2xto # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1254}' # _entry.id 2XTO # _exptl.entry_id 2XTO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 2XTO _cell.length_a 62.68 _cell.length_b 76.55 _cell.length_c 101.62 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XTO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D 1 1 B,E,F 2 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 ? 2 C N N ? 2 E 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 16 A SER 36 1_555 D MG MG . A MG 1257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 C O1B GDP . A GDP 1256 1_555 D MG MG . A MG 1257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 B OG SER 16 B SER 36 1_555 F MG MG . B MG 1255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc4 E O3B GDP . B GDP 1254 1_555 F MG MG . B MG 1255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _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 2XTO _atom_sites.fract_transf_matrix[1][1] 0.015954 _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] 0.013063 _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] 0.009841 _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 C 2 GDP A 1 1256 1256 GDP GDP . D 3 MG A 1 1257 1257 MG MG . E 2 GDP B 1 1254 1254 GDP GDP . F 3 MG B 1 1255 1255 MG MG . # 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 . . . E 2 15.12 10.646 0.879 1 21.2 ? PB GDP 1254 B 1 HETATM 2 O O1B GDP . . . E 2 13.997 11.595 1.22 1 20.68 ? O1B GDP 1254 B 1 HETATM 3 O O2B GDP . . . E 2 16.227 11.448 0.25 1 21.49 ? O2B GDP 1254 B 1 HETATM 4 O O3B GDP . . . E 2 14.653 9.594 -0.104 1 21.02 ? O3B GDP 1254 B 1 HETATM 5 O O3A GDP . . . E 2 15.745 9.921 2.184 1 21.67 ? O3A GDP 1254 B 1 HETATM 6 P PA GDP . . . E 2 14.886 9.436 3.456 1 20.94 ? PA GDP 1254 B 1 HETATM 7 O O1A GDP . . . E 2 14.353 8.041 3.26 1 21.62 ? O1A GDP 1254 B 1 HETATM 8 O O2A GDP . . . E 2 13.757 10.378 3.746 1 21.83 ? O2A GDP 1254 B 1 HETATM 9 O O5' GDP . . . E 2 15.945 9.493 4.66 1 21.64 ? O5' GDP 1254 B 1 HETATM 10 C C5' GDP . . . E 2 16.429 10.745 5.152 1 21.69 ? C5' GDP 1254 B 1 HETATM 11 C C4' GDP . . . E 2 16.471 10.776 6.682 1 21.75 ? C4' GDP 1254 B 1 HETATM 12 O O4' GDP . . . E 2 15.352 11.518 7.174 1 21.59 ? O4' GDP 1254 B 1 HETATM 13 C C3' GDP . . . E 2 16.399 9.398 7.328 1 21.98 ? C3' GDP 1254 B 1 HETATM 14 O O3' GDP . . . E 2 17.308 9.354 8.436 1 22.16 ? O3' GDP 1254 B 1 HETATM 15 C C2' GDP . . . E 2 14.971 9.297 7.822 1 21.83 ? C2' GDP 1254 B 1 HETATM 16 O O2' GDP . . . E 2 14.871 8.441 8.966 1 21.62 ? O2' GDP 1254 B 1 HETATM 17 C C1' GDP . . . E 2 14.651 10.747 8.145 1 21.85 ? C1' GDP 1254 B 1 HETATM 18 N N9 GDP . . . E 2 13.202 11.051 8.096 1 22.42 ? N9 GDP 1254 B 1 HETATM 19 C C8 GDP . . . E 2 12.37 10.914 7.043 1 22.35 ? C8 GDP 1254 B 1 HETATM 20 N N7 GDP . . . E 2 11.107 11.296 7.366 1 22.28 ? N7 GDP 1254 B 1 HETATM 21 C C5 GDP . . . E 2 11.124 11.693 8.651 1 22.63 ? C5 GDP 1254 B 1 HETATM 22 C C6 GDP . . . E 2 10.138 12.219 9.625 1 23.03 ? C6 GDP 1254 B 1 HETATM 23 O O6 GDP . . . E 2 8.943 12.379 9.289 1 23.7 ? O6 GDP 1254 B 1 HETATM 24 N N1 GDP . . . E 2 10.568 12.512 10.866 1 22.95 ? N1 GDP 1254 B 1 HETATM 25 C C2 GDP . . . E 2 11.856 12.343 11.251 1 22.97 ? C2 GDP 1254 B 1 HETATM 26 N N2 GDP . . . E 2 12.222 12.658 12.52 1 22.64 ? N2 GDP 1254 B 1 HETATM 27 N N3 GDP . . . E 2 12.811 11.867 10.407 1 22.67 ? N3 GDP 1254 B 1 HETATM 28 C C4 GDP . . . E 2 12.508 11.532 9.127 1 22.59 ? C4 GDP 1254 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #