data_4G5S # _model_server_result.job_id Iw_1SO0S_Ykt4FlS68tV1A _model_server_result.datetime_utc '2024-11-08 18:19:46' _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 4g5s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 4G5S # _exptl.entry_id 4G5S _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 3 _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 120 _cell.entry_id 4G5S _cell.length_a 209.68 _cell.length_b 209.68 _cell.length_c 235.482 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G5S _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J 1 1 B,H,K 2 1 C,F,L,M 3 1 D,G 4 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 I N N ? 3 K N N ? 3 L 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 103 n n PB O2B GDP sing 104 n n PB O3B GDP sing 105 n n PB O3A GDP sing 106 n n O2B HOB2 GDP sing 107 n n O3B HOB3 GDP sing 108 n n O3A PA GDP sing 109 n n PA O1A GDP doub 110 n n PA O2A GDP sing 111 n n PA O5' GDP sing 112 n n O2A HOA2 GDP sing 113 n n O5' C5' GDP sing 114 n n C5' C4' GDP sing 115 n n C5' H5' GDP sing 116 n n C5' "H5''" GDP sing 117 n n C4' O4' GDP sing 118 n n C4' C3' GDP sing 119 n n C4' H4' GDP sing 120 n n O4' C1' GDP sing 121 n n C3' O3' GDP sing 122 n n C3' C2' GDP sing 123 n n C3' H3' GDP sing 124 n n O3' HO3' GDP sing 125 n n C2' O2' GDP sing 126 n n C2' C1' GDP sing 127 n n C2' H2' GDP sing 128 n n O2' HO2' GDP sing 129 n n C1' N9 GDP sing 130 n n C1' H1' GDP sing 131 n n N9 C8 GDP sing 132 n y N9 C4 GDP sing 133 n y C8 N7 GDP doub 134 n y C8 H8 GDP sing 135 n n N7 C5 GDP sing 136 n y C5 C6 GDP sing 137 n n C5 C4 GDP doub 138 n y C6 O6 GDP doub 139 n n C6 N1 GDP sing 140 n n N1 C2 GDP sing 141 n n N1 HN1 GDP sing 142 n n C2 N2 GDP sing 143 n n C2 N3 GDP doub 144 n n N2 HN21 GDP sing 145 n n N2 HN22 GDP sing 146 n n N3 C4 GDP sing 147 n n # _atom_sites.entry_id 4G5S _atom_sites.fract_transf_matrix[1][1] 0.004769 _atom_sites.fract_transf_matrix[1][2] 0.002753 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005507 _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] 0.004247 _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 I 3 GDP A 1 401 1 GDP GDP . J 4 CIT A 1 402 1 CIT CIT . K 3 GDP B 1 401 1 GDP GDP . L 3 GDP C 1 401 1 GDP GDP . M 4 CIT C 1 402 1 CIT CIT . # 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 . . . I 3 -56.674 51.738 37.063 1 105.37 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . I 3 -56.533 53.044 37.797 1 84.29 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . I 3 -57.89 51.794 36.178 1 123.15 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . I 3 -55.454 51.482 36.223 1 120.82 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . I 3 -56.845 50.555 38.128 1 109.86 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . I 3 -55.585 50.07 38.988 1 116.69 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . I 3 -54.657 51.22 39.257 1 128.65 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . I 3 -54.853 48.971 38.266 1 68.71 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . I 3 -56.237 49.519 40.351 1 102.84 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . I 3 -55.802 50.052 41.602 1 110.81 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . I 3 -55.659 48.953 42.649 1 78.18 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . I 3 -56.908 48.3 42.86 1 101.95 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . I 3 -54.669 47.893 42.189 1 103.99 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . I 3 -53.495 47.932 43.004 1 146.33 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . I 3 -55.377 46.565 42.356 1 111.51 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . I 3 -54.591 45.683 43.16 1 162.05 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . I 3 -56.681 46.905 43.058 1 130.65 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . I 3 -57.809 46.129 42.493 1 111.83 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . I 3 -58.293 46.224 41.241 1 112.79 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . I 3 -59.337 45.377 41.063 1 136.61 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . I 3 -59.537 44.729 42.224 1 97.03 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . I 3 -60.477 43.703 42.728 1 108.9 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . I 3 -61.36 43.227 41.984 1 152.95 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . I 3 -60.346 43.298 43.998 1 109.43 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . I 3 -59.4 43.795 44.816 1 104.41 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . I 3 -59.331 43.337 46.088 1 89.15 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . I 3 -58.508 44.737 44.421 1 139.81 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . I 3 -58.53 45.232 43.163 1 114.17 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #