data_7EM4 # _model_server_result.job_id pA0gEn1y2Lu8MyblGdVnWA _model_server_result.datetime_utc '2024-11-28 14:16:43' _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 7em4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 7EM4 # _exptl.entry_id 7EM4 _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 7EM4 _cell.length_a 109.311 _cell.length_b 185.53 _cell.length_c 105.744 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EM4 _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,F _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 7EM4 _atom_sites.fract_transf_matrix[1][1] 0.009148 _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] 0.00539 _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] 0.009457 _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 . F 4 HOH A 1 601 601 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 C C2 CZU . . . D 3 57.383 48.506 -21.892 1 76.49 ? C2 CZU 502 A 1 HETATM 2 C C4 CZU . . . D 3 55.033 48.182 -22.117 1 69.14 ? C4 CZU 502 A 1 HETATM 3 C C5 CZU . . . D 3 55.182 46.902 -21.773 1 65.21 ? C5 CZU 502 A 1 HETATM 4 C C6 CZU . . . D 3 56.381 46.414 -21.506 1 66.93 ? C6 CZU 502 A 1 HETATM 5 O O6 CZU . . . D 3 56.497 45.237 -21.211 1 71.07 ? O6 CZU 502 A 1 HETATM 6 C C2' CZU . . . D 3 52.156 49.707 -24.646 1 71.27 ? C2' CZU 502 A 1 HETATM 7 C C3' CZU . . . D 3 51.137 50.793 -24.291 1 73.16 ? C3' CZU 502 A 1 HETATM 8 C C4' CZU . . . D 3 50.808 50.504 -22.838 1 69.14 ? C4' CZU 502 A 1 HETATM 9 C C5' CZU . . . D 3 49.971 49.242 -22.598 1 63.03 ? C5' CZU 502 A 1 HETATM 10 C C8 CZU . . . D 3 53.075 47.251 -22.145 1 65.66 ? C8 CZU 502 A 1 HETATM 11 N N1 CZU . . . D 3 57.521 47.229 -21.558 1 73.01 ? N1 CZU 502 A 1 HETATM 12 N N3 CZU . . . D 3 56.102 49 -22.18 1 73.73 ? N3 CZU 502 A 1 HETATM 13 N N7 CZU . . . D 3 53.978 46.33 -21.782 1 66.29 ? N7 CZU 502 A 1 HETATM 14 N N9 CZU . . . D 3 53.734 48.387 -22.35 1 65.77 ? N9 CZU 502 A 1 HETATM 15 O O1A CZU . . . D 3 50.266 47.122 -23.959 1 90.13 ? O1A CZU 502 A 1 HETATM 16 O O1B CZU . . . D 3 50.156 45.93 -26.116 1 83.68 ? O1B CZU 502 A 1 HETATM 17 O O1G CZU . . . D 3 45.981 45.663 -29.354 1 126.48 ? O1G CZU 502 A 1 HETATM 18 O O2' CZU . . . D 3 53.442 50.262 -24.88 1 70.29 ? O2' CZU 502 A 1 HETATM 19 O O2A CZU . . . D 3 48.244 46.788 -22.526 1 70.62 ? O2A CZU 502 A 1 HETATM 20 O O2B CZU . . . D 3 48.092 44.251 -25.685 1 61.46 ? O2B CZU 502 A 1 HETATM 21 O O2G CZU . . . D 3 45.503 44.94 -26.959 1 127.75 ? O2G CZU 502 A 1 HETATM 22 O O3' CZU . . . D 3 51.74 52.102 -24.377 1 72.89 ? O3' CZU 502 A 1 HETATM 23 O O3A CZU . . . D 3 48.03 47.033 -25.122 1 96.42 ? O3A CZU 502 A 1 HETATM 24 O O3B CZU . . . D 3 47.844 46.099 -27.51 1 121.38 ? O3B CZU 502 A 1 HETATM 25 O O3G CZU . . . D 3 45.552 47.452 -27.594 1 124.79 ? O3G CZU 502 A 1 HETATM 26 O O4' CZU . . . D 3 52.138 50.233 -22.319 1 62.18 ? O4' CZU 502 A 1 HETATM 27 O O5' CZU . . . D 3 48.872 49.032 -23.479 1 63.21 ? O5' CZU 502 A 1 HETATM 28 P PA CZU . . . D 3 48.737 47.506 -23.715 1 76.27 ? PA CZU 502 A 1 HETATM 29 P PB CZU . . . D 3 48.536 45.682 -26.034 1 101.21 ? PB CZU 502 A 1 HETATM 30 P PG CZU . . . D 3 46.197 46.134 -27.82 1 125.84 ? PG CZU 502 A 1 # _model_server_stats.io_time_ms 114 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #