data_3QI2 # _model_server_result.job_id WVyyPSE8Sm0y-mvJw0Hk4g _model_server_result.datetime_utc '2024-11-22 22:47:45' _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 3qi2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":355}' # _entry.id 3QI2 # _exptl.entry_id 3QI2 _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 3QI2 _cell.length_a 70.003 _cell.length_b 131.018 _cell.length_c 203.307 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QI2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 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 A,C,E,F,G,J,L 1 1 B,D,H,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 H 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 3QI2 _atom_sites.fract_transf_matrix[1][1] 0.014285 _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] 0.007633 _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] 0.004919 _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 1 355 355 GDP GDP . F 4 SO4 A 1 2 2 SO4 SO4 . G 5 GOL A 1 3 3 GOL GOL . H 3 GDP B 1 356 356 GDP GDP . I 4 SO4 B 1 1 1 SO4 SO4 . J 6 HOH A 1 4 4 HOH HOH . J 6 HOH A 2 6 6 HOH HOH . J 6 HOH A 3 7 7 HOH HOH . J 6 HOH A 4 8 8 HOH HOH . J 6 HOH A 5 12 12 HOH HOH . J 6 HOH A 6 14 14 HOH HOH . J 6 HOH A 7 15 15 HOH HOH . J 6 HOH A 8 17 17 HOH HOH . J 6 HOH A 9 19 19 HOH HOH . J 6 HOH A 10 20 20 HOH HOH . J 6 HOH A 11 25 25 HOH HOH . J 6 HOH A 12 356 3 HOH HOH . J 6 HOH A 13 357 27 HOH HOH . J 6 HOH A 14 358 29 HOH HOH . J 6 HOH A 15 359 31 HOH HOH . J 6 HOH A 16 360 33 HOH HOH . J 6 HOH A 17 361 35 HOH HOH . J 6 HOH A 18 362 36 HOH HOH . J 6 HOH A 19 363 38 HOH HOH . K 6 HOH B 1 2 2 HOH HOH . K 6 HOH B 2 5 5 HOH HOH . K 6 HOH B 3 10 10 HOH HOH . K 6 HOH B 4 11 11 HOH HOH . K 6 HOH B 5 13 13 HOH HOH . K 6 HOH B 6 16 16 HOH HOH . K 6 HOH B 7 18 18 HOH HOH . K 6 HOH B 8 21 21 HOH HOH . K 6 HOH B 9 26 26 HOH HOH . K 6 HOH B 10 355 1 HOH HOH . K 6 HOH B 11 357 28 HOH HOH . K 6 HOH B 12 358 34 HOH HOH . K 6 HOH B 13 359 39 HOH HOH . L 6 HOH C 1 22 22 HOH HOH . L 6 HOH C 2 32 32 HOH HOH . M 6 HOH D 1 9 9 HOH HOH . M 6 HOH D 2 30 30 HOH HOH . M 6 HOH D 3 37 37 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 . . . E 3 -28.004 17.097 29.685 1 31.49 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . E 3 -26.902 18.06 29.315 1 35.07 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . E 3 -28.653 16.557 28.435 1 36.46 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . E 3 -27.436 15.94 30.468 1 25.75 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . E 3 -29.104 17.847 30.586 1 60.53 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . E 3 -28.807 19.314 31.171 1 29.52 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . E 3 -28.576 20.292 30.045 1 41.1 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . E 3 -27.625 19.296 32.107 1 17.23 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . E 3 -30.166 19.677 31.95 1 34.64 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . E 3 -31.154 20.447 31.27 1 39.32 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . E 3 -31.851 21.387 32.24 1 34.83 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . E 3 -32.315 20.654 33.37 1 35.14 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . E 3 -30.884 22.441 32.753 1 64.53 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . E 3 -31.194 23.713 32.182 1 83.99 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . E 3 -31.081 22.484 34.252 1 68.61 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . E 3 -31.559 23.772 34.644 1 84.95 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . E 3 -32.127 21.425 34.557 1 49.99 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . E 3 -31.643 20.56 35.657 1 32.82 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . E 3 -30.606 19.704 35.596 1 29.25 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . E 3 -30.432 19.065 36.781 1 32.56 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . E 3 -31.381 19.514 37.623 1 33.46 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . E 3 -31.772 19.257 39.027 1 28.73 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . E 3 -31.144 18.433 39.724 1 42.92 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . E 3 -32.817 19.934 39.522 1 29.77 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . E 3 -33.51 20.827 38.789 1 37.8 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . E 3 -34.555 21.471 39.361 1 47.27 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . E 3 -33.209 21.113 37.497 1 34.12 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . E 3 -32.176 20.498 36.876 1 36.42 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #