data_1XD2 # _model_server_result.job_id TDxol3Atku8L6tX8tOKZng _model_server_result.datetime_utc '2024-11-23 05:09:57' _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 1xd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":169}' # _entry.id 1XD2 # _exptl.entry_id 1XD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 1XD2 _cell.length_a 183.703 _cell.length_b 183.703 _cell.length_c 177.804 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 6 _struct_asym.id F _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 metalc ? metalc1 A OG SER 17 A SER 17 1_555 D MG MG . A MG 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 D MG MG . A MG 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc3 D MG MG . A MG 167 1_555 E O4 PO4 . A PO4 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc4 D MG MG . A MG 167 1_555 F O3B GDP . A GDP 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? # _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 1XD2 _atom_sites.fract_transf_matrix[1][1] 0.005444 _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] 0.005444 _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] 0.005624 _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 D 4 MG A 1 167 2 MG MG2 . E 5 PO4 A 1 168 3 PO4 PO4 . F 6 GDP A 1 169 1 GDP GDP . G 5 PO4 B 1 167 4 PO4 PO4 . H 5 PO4 C 1 5 5 PO4 PO4 . I 5 PO4 C 1 6 6 PO4 PO4 . # 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 . . . F 6 14.975 53.297 67.816 1 28.18 ? PB GDP 169 A 1 HETATM 2 O O1B GDP . . . F 6 16.155 54.082 68.307 1 30.64 ? O1B GDP 169 A 1 HETATM 3 O O2B GDP . . . F 6 13.885 53.15 68.91 1 27.94 ? O2B GDP 169 A 1 HETATM 4 O O3B GDP . . . F 6 15.342 51.971 67.22 1 29.78 ? O3B GDP 169 A 1 HETATM 5 O O3A GDP . . . F 6 14.238 54.168 66.69 1 25.35 ? O3A GDP 169 A 1 HETATM 6 P PA GDP . . . F 6 13.437 53.703 65.455 1 26.16 ? PA GDP 169 A 1 HETATM 7 O O1A GDP . . . F 6 12.528 52.569 65.822 1 26.49 ? O1A GDP 169 A 1 HETATM 8 O O2A GDP . . . F 6 14.353 53.407 64.334 1 27.09 ? O2A GDP 169 A 1 HETATM 9 O O5' GDP . . . F 6 12.642 55.028 65.084 1 25.05 ? O5' GDP 169 A 1 HETATM 10 C C5' GDP . . . F 6 11.656 55.629 65.952 1 25.43 ? C5' GDP 169 A 1 HETATM 11 C C4' GDP . . . F 6 10.76 56.526 65.126 1 27.55 ? C4' GDP 169 A 1 HETATM 12 O O4' GDP . . . F 6 11.516 57.727 64.685 1 27.83 ? O4' GDP 169 A 1 HETATM 13 C C3' GDP . . . F 6 10.17 55.876 63.858 1 27.42 ? C3' GDP 169 A 1 HETATM 14 O O3' GDP . . . F 6 8.779 56.362 63.8 1 28.16 ? O3' GDP 169 A 1 HETATM 15 C C2' GDP . . . F 6 11.013 56.468 62.739 1 27.14 ? C2' GDP 169 A 1 HETATM 16 O O2' GDP . . . F 6 10.36 56.445 61.525 1 28.68 ? O2' GDP 169 A 1 HETATM 17 C C1' GDP . . . F 6 11.403 57.852 63.283 1 29.08 ? C1' GDP 169 A 1 HETATM 18 N N9 GDP . . . F 6 12.782 58.315 62.665 1 32.3 ? N9 GDP 169 A 1 HETATM 19 C C8 GDP . . . F 6 13.966 57.652 62.803 1 32.89 ? C8 GDP 169 A 1 HETATM 20 N N7 GDP . . . F 6 14.952 58.293 62.166 1 34.75 ? N7 GDP 169 A 1 HETATM 21 C C5 GDP . . . F 6 14.369 59.436 61.633 1 34.6 ? C5 GDP 169 A 1 HETATM 22 C C6 GDP . . . F 6 14.939 60.449 60.821 1 36.04 ? C6 GDP 169 A 1 HETATM 23 O O6 GDP . . . F 6 16.136 60.539 60.523 1 37.73 ? O6 GDP 169 A 1 HETATM 24 N N1 GDP . . . F 6 14.02 61.451 60.444 1 37.34 ? N1 GDP 169 A 1 HETATM 25 C C2 GDP . . . F 6 12.676 61.4 60.772 1 35.5 ? C2 GDP 169 A 1 HETATM 26 N N2 GDP . . . F 6 11.898 62.4 60.338 1 36.5 ? N2 GDP 169 A 1 HETATM 27 N N3 GDP . . . F 6 12.126 60.419 61.52 1 34.65 ? N3 GDP 169 A 1 HETATM 28 C C4 GDP . . . F 6 13.021 59.455 61.89 1 34.15 ? C4 GDP 169 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #