data_7EM1 # _model_server_result.job_id 7sgyZhRzTtSTwSzI5Mf9sQ _model_server_result.datetime_utc '2024-11-24 23:27:22' _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 7em1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 7EM1 # _exptl.entry_id 7EM1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 508.166 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _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 7EM1 _cell.length_a 109.192 _cell.length_b 186.857 _cell.length_c 104.65 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EM1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N4 O14 P3' _chem_comp.formula_weight 508.166 _chem_comp.id CZU _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "Inosine-5'-triphosphate" # 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 O1G PG CZU doub 83 n n O3G PG CZU sing 84 n n PG O3B CZU sing 85 n n PG O2G CZU sing 86 n n O3B PB CZU sing 87 n n O1B PB CZU doub 88 n n PB O2B CZU sing 89 n n PB O3A CZU sing 90 n n O2' C2' CZU sing 91 n n O3A PA CZU sing 92 n n O1A PA CZU doub 93 n n O3' C3' CZU sing 94 n n C3' C2' CZU sing 95 n n C3' C4' CZU sing 96 n n C2' C1' CZU sing 97 n n PA O5' CZU sing 98 n n PA O2A CZU sing 99 n n O5' C5' CZU sing 100 n n C1' N9 CZU sing 101 n n C1' O4' CZU sing 102 n n C4' C5' CZU sing 103 n n C4' O4' CZU sing 104 n n N9 C8 CZU sing 105 n y N9 C4 CZU sing 106 n y C8 N7 CZU doub 107 n y C4 N3 CZU sing 108 n n C4 C5 CZU doub 109 n y N3 C2 CZU doub 110 n n N7 C5 CZU sing 111 n y C5 C6 CZU sing 112 n n C2 N1 CZU sing 113 n n C6 N1 CZU sing 114 n n C6 O6 CZU doub 115 n n C2 H1 CZU sing 116 n n C1' H2 CZU sing 117 n n C2' H3 CZU sing 118 n n C3' H4 CZU sing 119 n n C4' H5 CZU sing 120 n n C5' H6 CZU sing 121 n n C5' H7 CZU sing 122 n n C8 H8 CZU sing 123 n n O2' H10 CZU sing 124 n n O2A H11 CZU sing 125 n n O2B H12 CZU sing 126 n n O2G H13 CZU sing 127 n n O3' H14 CZU sing 128 n n O3G H15 CZU sing 129 n n N1 H16 CZU sing 130 n n # _atom_sites.entry_id 7EM1 _atom_sites.fract_transf_matrix[1][1] 0.009158 _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] 0.005352 _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] 0.009556 _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 C 2 IDP A 1 501 501 IDP IDP . D 3 CZU A 1 502 502 CZU CZU . E 2 IDP B 1 501 501 IDP IDP . # 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 C C2 CZU . . . D 3 57.424 48.131 -21.622 1 89.51 ? C2 CZU 502 A 1 HETATM 2 C C4 CZU . . . D 3 55.078 47.945 -21.955 1 91.56 ? C4 CZU 502 A 1 HETATM 3 C C5 CZU . . . D 3 55.135 46.664 -21.569 1 89.66 ? C5 CZU 502 A 1 HETATM 4 C C6 CZU . . . D 3 56.293 46.117 -21.215 1 86.19 ? C6 CZU 502 A 1 HETATM 5 O O6 CZU . . . D 3 56.339 44.942 -20.865 1 88.95 ? O6 CZU 502 A 1 HETATM 6 C C1' CZU . . . D 3 53.258 49.542 -22.731 1 86.45 ? C1' CZU 502 A 1 HETATM 7 C C2' CZU . . . D 3 52.566 49.328 -24.069 1 88.53 ? C2' CZU 502 A 1 HETATM 8 C C3' CZU . . . D 3 51.562 50.417 -24.122 1 83.7 ? C3' CZU 502 A 1 HETATM 9 C C4' CZU . . . D 3 51.026 50.237 -22.698 1 81.53 ? C4' CZU 502 A 1 HETATM 10 C C5' CZU . . . D 3 50.318 48.902 -22.577 1 82.58 ? C5' CZU 502 A 1 HETATM 11 C C8 CZU . . . D 3 53.084 47.128 -22.046 1 90.26 ? C8 CZU 502 A 1 HETATM 12 N N1 CZU . . . D 3 57.469 46.869 -21.24 1 86.12 ? N1 CZU 502 A 1 HETATM 13 N N3 CZU . . . D 3 56.193 48.691 -21.981 1 91.16 ? N3 CZU 502 A 1 HETATM 14 N N7 CZU . . . D 3 53.9 46.161 -21.62 1 91.01 ? N7 CZU 502 A 1 HETATM 15 N N9 CZU . . . D 3 53.807 48.232 -22.249 1 89.99 ? N9 CZU 502 A 1 HETATM 16 O O1A CZU . . . D 3 49.846 46.918 -24.179 1 104.04 ? O1A CZU 502 A 1 HETATM 17 O O1B CZU . . . D 3 49.516 47.107 -26.806 1 105.62 ? O1B CZU 502 A 1 HETATM 18 O O1G CZU . . . D 3 45.521 45.774 -29.352 1 123.98 ? O1G CZU 502 A 1 HETATM 19 O O2' CZU . . . D 3 53.506 49.522 -25.106 1 92.71 ? O2' CZU 502 A 1 HETATM 20 O O2A CZU . . . D 3 47.8 46.865 -22.657 1 99.68 ? O2A CZU 502 A 1 HETATM 21 O O2B CZU . . . D 3 47.753 45.443 -26.104 1 124.18 ? O2B CZU 502 A 1 HETATM 22 O O2G CZU . . . D 3 44.949 45.7 -26.894 1 123.39 ? O2G CZU 502 A 1 HETATM 23 O O3' CZU . . . D 3 52.248 51.65 -24.283 1 79.7 ? O3' CZU 502 A 1 HETATM 24 O O3A CZU . . . D 3 47.672 47.886 -25.125 1 110.09 ? O3A CZU 502 A 1 HETATM 25 O O3B CZU . . . D 3 46.939 47.357 -27.703 1 119.71 ? O3B CZU 502 A 1 HETATM 26 O O3G CZU . . . D 3 44.347 47.787 -28.239 1 125.35 ? O3G CZU 502 A 1 HETATM 27 O O4' CZU . . . D 3 52.233 50.163 -21.894 1 81.13 ? O4' CZU 502 A 1 HETATM 28 O O5' CZU . . . D 3 49.025 48.996 -23.13 1 89.87 ? O5' CZU 502 A 1 HETATM 29 P PA CZU . . . D 3 48.486 47.659 -23.689 1 99.19 ? PA CZU 502 A 1 HETATM 30 P PB CZU . . . D 3 47.957 46.884 -26.429 1 118.73 ? PB CZU 502 A 1 HETATM 31 P PG CZU . . . D 3 45.391 46.741 -28.042 1 124.77 ? PG CZU 502 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 31 #