data_4G5R # _model_server_result.job_id E8Egye2KYgMqgJmGh5ck1Q _model_server_result.datetime_utc '2024-11-08 18:40:13' _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 4g5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 4G5R # _exptl.entry_id 4G5R _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 4 _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 4G5R _cell.length_a 209.55 _cell.length_b 209.55 _cell.length_c 237.211 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G5R _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,F,K,L,M,N 2 1 C,G,O,P,Q,R 3 1 D,H,S 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 O N N ? 3 S 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 4G5R _atom_sites.fract_transf_matrix[1][1] 0.004772 _atom_sites.fract_transf_matrix[1][2] 0.002755 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00551 _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] 0.004216 _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 SO4 A 1 402 3 SO4 SO4 . K 3 GDP B 1 401 1 GDP GDP . L 5 CIT B 1 402 1 CIT CIT . M 5 CIT B 1 403 1 CIT CIT . N 4 SO4 B 1 404 1 SO4 SO4 . O 3 GDP C 1 401 1 GDP GDP . P 5 CIT C 1 402 1 CIT CIT . Q 5 CIT C 1 403 1 CIT CIT . R 4 SO4 C 1 404 2 SO4 SO4 . S 3 GDP D 1 401 1 GDP GDP . # 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 . . . O 3 -69.299 -66.683 5.2 1 85.29 ? PB GDP 401 C 1 HETATM 2 O O1B GDP . . . O 3 -70.795 -66.63 5.018 1 60.74 ? O1B GDP 401 C 1 HETATM 3 O O2B GDP . . . O 3 -68.663 -67.302 3.98 1 100.4 ? O2B GDP 401 C 1 HETATM 4 O O3B GDP . . . O 3 -68.764 -65.285 5.408 1 76.97 ? O3B GDP 401 C 1 HETATM 5 O O3A GDP . . . O 3 -68.961 -67.604 6.467 1 82.67 ? O3A GDP 401 C 1 HETATM 6 P PA GDP . . . O 3 -68.927 -66.985 7.941 1 78.61 ? PA GDP 401 C 1 HETATM 7 O O1A GDP . . . O 3 -70.086 -66.047 8.17 1 90.85 ? O1A GDP 401 C 1 HETATM 8 O O2A GDP . . . O 3 -67.618 -66.26 8.145 1 65.02 ? O2A GDP 401 C 1 HETATM 9 O O5' GDP . . . O 3 -69.054 -68.293 8.873 1 78.83 ? O5' GDP 401 C 1 HETATM 10 C C5' GDP . . . O 3 -70.305 -68.587 9.501 1 79.64 ? C5' GDP 401 C 1 HETATM 11 C C4' GDP . . . O 3 -70.082 -69.303 10.826 1 80.18 ? C4' GDP 401 C 1 HETATM 12 O O4' GDP . . . O 3 -69.387 -70.53 10.613 1 87.86 ? O4' GDP 401 C 1 HETATM 13 C C3' GDP . . . O 3 -69.233 -68.451 11.754 1 77.02 ? C3' GDP 401 C 1 HETATM 14 O O3' GDP . . . O 3 -70.004 -68.06 12.892 1 91.54 ? O3' GDP 401 C 1 HETATM 15 C C2' GDP . . . O 3 -68.085 -69.33 12.189 1 84.02 ? C2' GDP 401 C 1 HETATM 16 O O2' GDP . . . O 3 -68.054 -69.409 13.613 1 110.31 ? O2' GDP 401 C 1 HETATM 17 C C1' GDP . . . O 3 -68.375 -70.704 11.607 1 94.92 ? C1' GDP 401 C 1 HETATM 18 N N9 GDP . . . O 3 -67.147 -71.268 10.993 1 83.25 ? N9 GDP 401 C 1 HETATM 19 C C8 GDP . . . O 3 -66.537 -70.782 9.896 1 83.84 ? C8 GDP 401 C 1 HETATM 20 N N7 GDP . . . O 3 -65.445 -71.522 9.581 1 87.32 ? N7 GDP 401 C 1 HETATM 21 C C5 GDP . . . O 3 -65.345 -72.507 10.486 1 84.51 ? C5 GDP 401 C 1 HETATM 22 C C6 GDP . . . O 3 -64.418 -73.634 10.721 1 80.24 ? C6 GDP 401 C 1 HETATM 23 O O6 GDP . . . O 3 -63.448 -73.828 9.964 1 82.19 ? O6 GDP 401 C 1 HETATM 24 N N1 GDP . . . O 3 -64.656 -74.434 11.765 1 69.56 ? N1 GDP 401 C 1 HETATM 25 C C2 GDP . . . O 3 -65.701 -74.237 12.59 1 68.11 ? C2 GDP 401 C 1 HETATM 26 N N2 GDP . . . O 3 -65.867 -75.093 13.625 1 74.97 ? N2 GDP 401 C 1 HETATM 27 N N3 GDP . . . O 3 -66.594 -73.223 12.433 1 71.95 ? N3 GDP 401 C 1 HETATM 28 C C4 GDP . . . O 3 -66.47 -72.34 11.415 1 77.2 ? C4 GDP 401 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #