data_5NYZ # _model_server_result.job_id Hva9icC7TjZpUTgX-pddqg _model_server_result.datetime_utc '2025-08-31 05:55:32' _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 5nyz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5NYZ # _exptl.entry_id 5NYZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 5NYZ _cell.length_a 87.27 _cell.length_b 87.27 _cell.length_c 87.27 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NYZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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 -z+1/2,-x,y+1/2 0 0 -1 -1 0 0 0 1 0 43.635 0 43.635 3 'crystal symmetry operation' 10_545 -y,z-1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 0 -43.635 43.635 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OE1 GLU 95 A GLU 95 1_555 D MG MG . A MG 203 10_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 B O2A DUP . A DUP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc3 B O2B DUP . A DUP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc4 B O1G DUP . A DUP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc5 D MG MG . A MG 203 1_555 E O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? metalc ? metalc6 D MG MG . A MG 203 1_555 E O HOH . A HOH 304 10_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _chem_comp.type non-polymer _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 O4 C4 DUP doub 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 5NYZ _atom_sites.fract_transf_matrix[1][1] 0.011459 _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] 0.011459 _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] 0.011459 _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 B 2 DUP A 1 201 1173 DUP DUP . C 3 MG A 1 202 2 MG MG . D 3 MG A 1 203 3 MG MG . E 4 HOH A 1 301 62 HOH HOH . E 4 HOH A 2 302 11 HOH HOH . E 4 HOH A 3 303 17 HOH HOH . E 4 HOH A 4 304 1 HOH HOH . E 4 HOH A 5 305 59 HOH HOH . E 4 HOH A 6 306 16 HOH HOH . E 4 HOH A 7 307 27 HOH HOH . E 4 HOH A 8 308 18 HOH HOH . E 4 HOH A 9 309 61 HOH HOH . E 4 HOH A 10 310 6 HOH HOH . E 4 HOH A 11 311 57 HOH HOH . E 4 HOH A 12 312 2 HOH HOH . E 4 HOH A 13 313 3 HOH HOH . E 4 HOH A 14 314 4 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 O O4 DUP . . . B 2 5.279 7.67 36.97 1 79.59 ? O4 DUP 201 A 1 HETATM 2 C C4 DUP . . . B 2 5.603 8.766 37.472 1 80 ? C4 DUP 201 A 1 HETATM 3 C C5 DUP . . . B 2 6.151 8.797 38.749 1 80.33 ? C5 DUP 201 A 1 HETATM 4 C C6 DUP . . . B 2 6.515 10.02 39.312 1 80.48 ? C6 DUP 201 A 1 HETATM 5 N N3 DUP . . . B 2 5.423 9.91 36.789 1 80.39 ? N3 DUP 201 A 1 HETATM 6 C C2 DUP . . . B 2 5.766 11.1 37.314 1 79.11 ? C2 DUP 201 A 1 HETATM 7 O O2 DUP . . . B 2 5.575 12.126 36.623 1 76.93 ? O2 DUP 201 A 1 HETATM 8 N N1 DUP . . . B 2 6.34 11.165 38.618 1 80.18 ? N1 DUP 201 A 1 HETATM 9 C C1' DUP . . . B 2 6.715 12.453 39.233 1 79.38 ? C1' DUP 201 A 1 HETATM 10 C C2' DUP . . . B 2 5.679 12.802 40.296 1 78.47 ? C2' DUP 201 A 1 HETATM 11 C C3' DUP . . . B 2 6.431 12.971 41.596 1 77.72 ? C3' DUP 201 A 1 HETATM 12 O O3' DUP . . . B 2 6.05 14.161 42.283 1 76.7 ? O3' DUP 201 A 1 HETATM 13 O O4' DUP . . . B 2 7.99 12.401 39.887 1 78.81 ? O4' DUP 201 A 1 HETATM 14 C C4' DUP . . . B 2 7.902 12.981 41.195 1 78.35 ? C4' DUP 201 A 1 HETATM 15 C C5' DUP . . . B 2 8.787 12.231 42.182 1 78.6 ? C5' DUP 201 A 1 HETATM 16 O O5' DUP . . . B 2 8.179 11.001 42.573 1 79.99 ? O5' DUP 201 A 1 HETATM 17 P PA DUP . . . B 2 8.957 10.029 43.578 1 79.74 ? PA DUP 201 A 1 HETATM 18 O O1A DUP . . . B 2 8.161 8.807 43.82 1 80.5 ? O1A DUP 201 A 1 HETATM 19 O O2A DUP . . . B 2 9.25 10.792 44.965 1 80.13 ? O2A DUP 201 A 1 HETATM 20 N N3A DUP . . . B 2 10.452 9.656 42.765 1 79.3 ? N3A DUP 201 A 1 HETATM 21 P PB DUP . . . B 2 11.968 10.098 43.468 1 79.52 ? PB DUP 201 A 1 HETATM 22 O O1B DUP . . . B 2 13.024 9.182 42.984 1 80.08 ? O1B DUP 201 A 1 HETATM 23 O O2B DUP . . . B 2 11.834 10.048 45.073 1 81.19 ? O2B DUP 201 A 1 HETATM 24 O O3B DUP . . . B 2 12.282 11.581 42.921 1 82.93 ? O3B DUP 201 A 1 HETATM 25 P PG DUP . . . B 2 12.491 12.858 43.879 1 81.15 ? PG DUP 201 A 1 HETATM 26 O O2G DUP . . . B 2 12.216 14.02 42.953 1 80.53 ? O2G DUP 201 A 1 HETATM 27 O O1G DUP . . . B 2 11.472 12.698 44.986 1 80.87 ? O1G DUP 201 A 1 HETATM 28 O O3G DUP . . . B 2 13.93 12.72 44.319 1 80.13 ? O3G DUP 201 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #