data_2XNS # _model_server_result.job_id w_hJLFabovzey01LvBohdw _model_server_result.datetime_utc '2024-10-11 00:30:53' _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 2xns # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1348}' # _entry.id 2XNS # _exptl.entry_id 2XNS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 2XNS _cell.length_a 265.261 _cell.length_b 265.261 _cell.length_c 265.261 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XNS _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,D,G,H,J,L,N 1 1 A,C,E,F,I,K,M 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 ? 3 E N N ? 3 G N N # _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 2XNS _atom_sites.fract_transf_matrix[1][1] 0.00377 _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] 0.00377 _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] 0.00377 _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 E 3 GDP A 1 1348 1348 GDP GDP . F 4 SRT A 1 1349 1349 SRT SRT . G 3 GDP B 1 1348 1348 GDP GDP . H 4 SRT B 1 1349 1349 SRT SRT . I 5 SO4 C 1 1535 1535 SO4 SO4 . J 5 SO4 D 1 1535 1535 SO4 SO4 . K 6 HOH A 1 2001 2001 HOH HOH . K 6 HOH A 2 2002 2002 HOH HOH . K 6 HOH A 3 2003 2003 HOH HOH . K 6 HOH A 4 2004 2004 HOH HOH . L 6 HOH B 1 2001 2001 HOH HOH . L 6 HOH B 2 2002 2002 HOH HOH . L 6 HOH B 3 2003 2003 HOH HOH . L 6 HOH B 4 2004 2004 HOH HOH . M 6 HOH C 1 2001 2001 HOH HOH . N 6 HOH D 1 2001 2001 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 . . . G 3 -15.09 36.46 149.534 1 96.33 ? PB GDP 1348 B 1 HETATM 2 O O1B GDP . . . G 3 -15.213 35.784 150.879 1 96.3 ? O1B GDP 1348 B 1 HETATM 3 O O2B GDP . . . G 3 -15.334 35.461 148.43 1 96.59 ? O2B GDP 1348 B 1 HETATM 4 O O3B GDP . . . G 3 -13.695 37.005 149.36 1 96.68 ? O3B GDP 1348 B 1 HETATM 5 O O3A GDP . . . G 3 -16.151 37.666 149.466 1 95.16 ? O3A GDP 1348 B 1 HETATM 6 P PA GDP . . . G 3 -17.342 37.644 148.384 1 94.23 ? PA GDP 1348 B 1 HETATM 7 O O1A GDP . . . G 3 -18.226 38.855 148.561 1 94.61 ? O1A GDP 1348 B 1 HETATM 8 O O2A GDP . . . G 3 -18.166 36.392 148.545 1 93.98 ? O2A GDP 1348 B 1 HETATM 9 O O5' GDP . . . G 3 -16.538 37.706 146.989 1 92.73 ? O5' GDP 1348 B 1 HETATM 10 C C5' GDP . . . G 3 -17.192 37.465 145.753 1 91.29 ? C5' GDP 1348 B 1 HETATM 11 C C4' GDP . . . G 3 -17.633 38.762 145.072 1 90.4 ? C4' GDP 1348 B 1 HETATM 12 O O4' GDP . . . G 3 -18.099 38.467 143.756 1 90.09 ? O4' GDP 1348 B 1 HETATM 13 C C3' GDP . . . G 3 -18.82 39.422 145.741 1 90 ? C3' GDP 1348 B 1 HETATM 14 O O3' GDP . . . G 3 -18.8 40.8 145.376 1 90.75 ? O3' GDP 1348 B 1 HETATM 15 C C2' GDP . . . G 3 -20.023 38.746 145.123 1 89.86 ? C2' GDP 1348 B 1 HETATM 16 O O2' GDP . . . G 3 -21.162 39.614 145.034 1 90.23 ? O2' GDP 1348 B 1 HETATM 17 C C1' GDP . . . G 3 -19.525 38.324 143.747 1 89.44 ? C1' GDP 1348 B 1 HETATM 18 N N9 GDP . . . G 3 -19.903 36.911 143.472 1 88.54 ? N9 GDP 1348 B 1 HETATM 19 C C8 GDP . . . G 3 -19.753 35.854 144.298 1 88.14 ? C8 GDP 1348 B 1 HETATM 20 N N7 GDP . . . G 3 -20.212 34.715 143.733 1 87.61 ? N7 GDP 1348 B 1 HETATM 21 C C5 GDP . . . G 3 -20.673 35.042 142.519 1 87.47 ? C5 GDP 1348 B 1 HETATM 22 C C6 GDP . . . G 3 -21.293 34.322 141.395 1 87.64 ? C6 GDP 1348 B 1 HETATM 23 O O6 GDP . . . G 3 -21.483 33.092 141.489 1 88.53 ? O6 GDP 1348 B 1 HETATM 24 N N1 GDP . . . G 3 -21.635 35.017 140.297 1 87.03 ? N1 GDP 1348 B 1 HETATM 25 C C2 GDP . . . G 3 -21.429 36.341 140.197 1 86.64 ? C2 GDP 1348 B 1 HETATM 26 N N2 GDP . . . G 3 -21.789 36.99 139.067 1 86.41 ? N2 GDP 1348 B 1 HETATM 27 N N3 GDP . . . G 3 -20.863 37.062 141.192 1 87.19 ? N3 GDP 1348 B 1 HETATM 28 C C4 GDP . . . G 3 -20.468 36.48 142.347 1 87.63 ? C4 GDP 1348 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #