data_6YOM # _model_server_result.job_id GB_SsOjgR_HgN-FLUVUUCQ _model_server_result.datetime_utc '2025-06-21 01:28:32' _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 6yom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":707}' # _entry.id 6YOM # _exptl.entry_id 6YOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 524.165 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _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 6YOM _cell.length_a 105.298 _cell.length_b 105.298 _cell.length_c 195.629 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 P N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 61 A HIS 167 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc2 A NE2 HIS 100 A HIS 206 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A OD2 ASP 101 A ASP 207 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A OD1 ASP 101 A ASP 207 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A NE2 HIS 127 A HIS 233 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 A OD1 ASP 205 A ASP 311 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc7 C FE FE . A FE 701 1_555 G O2A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc8 D MN MN . A MN 702 1_555 G O1A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 E MG MG . A MG 703 1_555 G O3G 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 E MG MG . A MG 703 1_555 G O1B 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc11 F MG MG . A MG 704 1_555 H O9 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc12 F MG MG . A MG 704 1_555 H O12 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc13 F MG MG . A MG 704 1_555 H O14 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc14 F MG MG . A MG 704 1_555 J O2B DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc15 F MG MG . A MG 704 1_555 J O1G DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc16 I O3G DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc17 I O1B DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc18 B NE2 HIS 61 B HIS 167 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc19 B NE2 HIS 100 B HIS 206 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc20 B OD2 ASP 101 B ASP 207 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc21 B OD1 ASP 101 B ASP 207 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc22 B NE2 HIS 127 B HIS 233 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc23 B OD1 ASP 205 B ASP 311 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 K FE FE . B FE 702 1_555 O O2A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc25 L MN MN . B MN 703 1_555 O O1A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc26 M MG MG . B MG 704 1_555 O O1B 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc27 M MG MG . B MG 704 1_555 O O3G 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc28 N MG MG . B MG 705 1_555 P O9 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc29 N MG MG . B MG 705 1_555 P O14 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc30 N MG MG . B MG 705 1_555 P O12 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? # _chem_comp.formula 'C10 H15 N4 O15 P3' _chem_comp.formula_weight 524.165 _chem_comp.id CZF _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'xanthosine 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 O15 P3 CZF doub 129 n n P3 O10 CZF sing 130 n n P3 O14 CZF sing 131 n n P3 O13 CZF sing 132 n n O10 P2 CZF sing 133 n n O12 P2 CZF doub 134 n n P2 O11 CZF sing 135 n n P2 O7 CZF sing 136 n n O8 P1 CZF doub 137 n n O7 P1 CZF sing 138 n n P1 O9 CZF sing 139 n n P1 O5 CZF sing 140 n n O5 C8 CZF sing 141 n n C8 C6 CZF sing 142 n n C4 C3 CZF sing 143 n n C4 C6 CZF sing 144 n n C4 O3 CZF sing 145 n n C3 O2 CZF sing 146 n n C3 C1 CZF sing 147 n n O4 C6 CZF sing 148 n n O4 C1 CZF sing 149 n n C1 N4 CZF sing 150 n n N4 C10 CZF sing 151 n y N4 C5 CZF sing 152 n y C10 N3 CZF doub 153 n y C5 N2 CZF sing 154 n n C5 C7 CZF doub 155 n y N3 C7 CZF sing 156 n y N2 C2 CZF sing 157 n n C7 C9 CZF sing 158 n n C2 O1 CZF doub 159 n n C2 N1 CZF sing 160 n n C9 N1 CZF sing 161 n n C9 O6 CZF doub 162 n n C1 H1 CZF sing 163 n n C3 H2 CZF sing 164 n n C4 H3 CZF sing 165 n n C6 H4 CZF sing 166 n n C8 H5 CZF sing 167 n n C8 H6 CZF sing 168 n n C10 H7 CZF sing 169 n n N1 H8 CZF sing 170 n n N2 H9 CZF sing 171 n n O2 H10 CZF sing 172 n n O3 H11 CZF sing 173 n n O9 H12 CZF sing 174 n n O11 H13 CZF sing 175 n n O13 H14 CZF sing 176 n n O14 H15 CZF sing 177 n n # _atom_sites.entry_id 6YOM _atom_sites.fract_transf_matrix[1][1] 0.009497 _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] 0.009497 _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] 0.005112 _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 FE A 1 701 701 FE FE . D 3 MN A 1 702 702 MN MN . E 4 MG A 1 703 703 MG MG . F 4 MG A 1 704 704 MG MG . G 5 0KX A 1 705 801 0KX dCN . H 6 CZF A 1 706 802 CZF XTP . I 7 DTP A 1 707 803 DTP DTP . J 7 DTP B 1 701 803 DTP DTP . K 2 FE B 1 702 701 FE FE . L 3 MN B 1 703 702 MN MN . M 4 MG B 1 704 703 MG MG . N 4 MG B 1 705 704 MG MG . O 5 0KX B 1 706 801 0KX dCN . P 6 CZF B 1 707 802 CZF XTP . # 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 C1 CZF . . . P 6 2.214 -22.646 -8.521 1 59.24 ? C1 CZF 707 B 1 HETATM 2 C C2 CZF . . . P 6 0.653 -25.049 -12.142 1 60.81 ? C2 CZF 707 B 1 HETATM 3 C C3 CZF . . . P 6 0.932 -23.169 -7.856 1 58.71 ? C3 CZF 707 B 1 HETATM 4 C C4 CZF . . . P 6 1.37 -24.507 -7.256 1 59.9 ? C4 CZF 707 B 1 HETATM 5 C C5 CZF . . . P 6 1.587 -23.216 -10.968 1 59.28 ? C5 CZF 707 B 1 HETATM 6 C C6 CZF . . . P 6 2.866 -24.283 -7.062 1 61.19 ? C6 CZF 707 B 1 HETATM 7 C C7 CZF . . . P 6 1.695 -22.498 -12.148 1 59.07 ? C7 CZF 707 B 1 HETATM 8 C C8 CZF . . . P 6 3.682 -25.529 -6.845 1 65.62 ? C8 CZF 707 B 1 HETATM 9 C C9 CZF . . . P 6 1.29 -23.048 -13.379 1 59.86 ? C9 CZF 707 B 1 HETATM 10 C C10 CZF . . . P 6 2.452 -21.227 -10.588 1 60.38 ? C10 CZF 707 B 1 HETATM 11 N N1 CZF . . . P 6 0.774 -24.332 -13.299 1 60.93 ? N1 CZF 707 B 1 HETATM 12 N N2 CZF . . . P 6 1.076 -24.469 -10.973 1 60.01 ? N2 CZF 707 B 1 HETATM 13 N N3 CZF . . . P 6 2.241 -21.249 -11.883 1 60.73 ? N3 CZF 707 B 1 HETATM 14 N N4 CZF . . . P 6 2.084 -22.395 -9.959 1 59.5 ? N4 CZF 707 B 1 HETATM 15 O O1 CZF . . . P 6 0.182 -26.172 -12.149 1 61.38 ? O1 CZF 707 B 1 HETATM 16 O O2 CZF . . . P 6 0.458 -22.288 -6.861 1 55.94 ? O2 CZF 707 B 1 HETATM 17 O O3 CZF . . . P 6 0.721 -24.802 -6.029 1 60.64 ? O3 CZF 707 B 1 HETATM 18 O O4 CZF . . . P 6 3.236 -23.601 -8.289 1 59.11 ? O4 CZF 707 B 1 HETATM 19 O O5 CZF . . . P 6 3.634 -26.313 -8.056 1 72.28 ? O5 CZF 707 B 1 HETATM 20 O O6 CZF . . . P 6 1.369 -22.514 -14.481 1 60.87 ? O6 CZF 707 B 1 HETATM 21 O O7 CZF . . . P 6 4.111 -28.646 -7.32 1 71.89 ? O7 CZF 707 B 1 HETATM 22 O O8 CZF . . . P 6 3.084 -28.187 -9.581 1 77.46 ? O8 CZF 707 B 1 HETATM 23 O O9 CZF . . . P 6 1.713 -27.825 -7.434 1 73.32 -1 O9 CZF 707 B 1 HETATM 24 O O10 CZF . . . P 6 3.035 -30.82 -7.005 1 73.49 ? O10 CZF 707 B 1 HETATM 25 O O11 CZF . . . P 6 5.19 -30.269 -5.704 1 74.51 ? O11 CZF 707 B 1 HETATM 26 O O12 CZF . . . P 6 2.941 -29.149 -5.12 1 68.41 -1 O12 CZF 707 B 1 HETATM 27 O O13 CZF . . . P 6 0.808 -31.545 -8.025 1 70.97 -1 O13 CZF 707 B 1 HETATM 28 O O14 CZF . . . P 6 0.96 -30.794 -5.64 1 74.93 ? O14 CZF 707 B 1 HETATM 29 O O15 CZF . . . P 6 1.987 -32.974 -6.275 1 74.44 -1 O15 CZF 707 B 1 HETATM 30 P P1 CZF . . . P 6 3.03 -27.787 -8.145 1 74.18 ? P1 CZF 707 B 1 HETATM 31 P P2 CZF . . . P 6 3.859 -29.724 -6.157 1 74.5 ? P2 CZF 707 B 1 HETATM 32 P P3 CZF . . . P 6 1.619 -31.578 -6.738 1 72.31 ? P3 CZF 707 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #