data_9J1O # _model_server_result.job_id nxfq4-DtRPDWZZH87KBGOg _model_server_result.datetime_utc '2025-06-20 13:46:47' _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 9j1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 9J1O # _exptl.entry_id 9J1O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 9J1O _cell.length_a 33.2 _cell.length_b 54.87 _cell.length_c 100.79 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H,I _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 5 _struct_asym.id E _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 covale ? covale1 A P DT 1 A DT 2 1_555 D O3' 3D1 . A 3D1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale2 B P DC 1 B DC 2 1_555 E O3' THM . B THM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? hydrog WATSON-CRICK hydrog1 A N3 DT 1 A DT 2 1_555 B N1 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 2 1_555 B N6 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 2 A DG 3 1_555 B N3 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 2 A DG 3 1_555 B O2 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 2 A DG 3 1_555 B N4 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 4 1_555 B N3 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 4 1_555 B O4 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 4 A DA 5 1_555 B N3 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 4 A DA 5 1_555 B O4 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 5 A DA 6 1_555 B N3 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 5 A DA 6 1_555 B O4 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 6 A DA 7 1_555 B N3 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 6 A DA 7 1_555 B O4 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 7 A DG 8 1_555 B N3 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 7 A DG 8 1_555 B O2 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 7 A DG 8 1_555 B N4 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DG 8 A DG 9 1_555 B N3 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 DG 8 A DG 9 1_555 B O2 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 DG 8 A DG 9 1_555 B N4 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 9 A DG 10 1_555 B N3 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 9 A DG 10 1_555 B O2 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 9 A DG 10 1_555 B N4 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 10 A DA 11 1_555 B N3 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 10 A DA 11 1_555 B O4 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DA 11 A DA 12 1_555 B N3 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 DA 11 A DA 12 1_555 B O4 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DT 12 A DT 13 1_555 B N1 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 DT 12 A DT 13 1_555 B N6 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 DT 13 A DT 14 1_555 B N1 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O4 DT 13 A DT 14 1_555 B N6 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 DG 14 A DG 15 1_555 B N3 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N2 DG 14 A DG 15 1_555 B O2 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O6 DG 14 A DG 15 1_555 B N4 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 DG 15 A DG 16 1_555 B N3 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N2 DG 15 A DG 16 1_555 B O2 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O6 DG 15 A DG 16 1_555 B N4 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 502 n n O5' HO5' THM sing 503 n n C5' C4' THM sing 504 n n C5' "H5'1" THM sing 505 n n C5' "H5'2" THM sing 506 n n C4' O4' THM sing 507 n n C4' C3' THM sing 508 n n C4' H4' THM sing 509 n n O4' C1' THM sing 510 n n C3' O3' THM sing 511 n n C3' C2' THM sing 512 n n C3' H3' THM sing 513 n n O3' HO3' THM sing 514 n n C2' C1' THM sing 515 n n C2' "H2'1" THM sing 516 n n C2' "H2'2" THM sing 517 n n C1' N1 THM sing 518 n n C1' H1' THM sing 519 n n N1 C2 THM sing 520 n n N1 C6 THM sing 521 n n C2 O2 THM doub 522 n n C2 N3 THM sing 523 n n N3 C4 THM sing 524 n n N3 HN3 THM sing 525 n n C4 O4 THM doub 526 n n C4 C5 THM sing 527 n n C5 C5M THM sing 528 n n C5 C6 THM doub 529 n n C5M HM51 THM sing 530 n n C5M HM52 THM sing 531 n n C5M HM53 THM sing 532 n n C6 H6 THM sing 533 n n # _atom_sites.entry_id 9J1O _atom_sites.fract_transf_matrix[1][1] 0.03012 _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] 0.018225 _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] 0.009922 _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 D 4 3D1 A 1 101 1 3D1 3D1 . E 5 THM B 1 101 1 THM THM . F 6 PG4 B 1 102 1 PG4 PG4 . G 7 HOH A 1 201 28 HOH HOH . G 7 HOH A 2 202 10 HOH HOH . G 7 HOH A 3 203 43 HOH HOH . G 7 HOH A 4 204 39 HOH HOH . G 7 HOH A 5 205 29 HOH HOH . G 7 HOH A 6 206 21 HOH HOH . G 7 HOH A 7 207 33 HOH HOH . G 7 HOH A 8 208 34 HOH HOH . H 7 HOH B 1 201 12 HOH HOH . H 7 HOH B 2 202 25 HOH HOH . H 7 HOH B 3 203 22 HOH HOH . H 7 HOH B 4 204 9 HOH HOH . H 7 HOH B 5 205 17 HOH HOH . H 7 HOH B 6 206 35 HOH HOH . H 7 HOH B 7 207 15 HOH HOH . H 7 HOH B 8 208 40 HOH HOH . H 7 HOH B 9 209 14 HOH HOH . H 7 HOH B 10 210 4 HOH HOH . H 7 HOH B 11 211 18 HOH HOH . H 7 HOH B 12 212 13 HOH HOH . H 7 HOH B 13 213 27 HOH HOH . H 7 HOH B 14 214 44 HOH HOH . I 7 HOH C 1 301 19 HOH HOH . I 7 HOH C 2 302 1 HOH HOH . I 7 HOH C 3 303 7 HOH HOH . I 7 HOH C 4 304 8 HOH HOH . I 7 HOH C 5 305 3 HOH HOH . I 7 HOH C 6 306 5 HOH HOH . I 7 HOH C 7 307 31 HOH HOH . I 7 HOH C 8 308 6 HOH HOH . I 7 HOH C 9 309 30 HOH HOH . I 7 HOH C 10 310 23 HOH HOH . I 7 HOH C 11 311 2 HOH HOH . I 7 HOH C 12 312 16 HOH HOH . I 7 HOH C 13 313 20 HOH HOH . I 7 HOH C 14 314 24 HOH HOH . I 7 HOH C 15 315 37 HOH HOH . I 7 HOH C 16 316 41 HOH HOH . I 7 HOH C 17 317 36 HOH HOH . I 7 HOH C 18 318 26 HOH HOH . I 7 HOH C 19 319 11 HOH HOH . I 7 HOH C 20 320 45 HOH HOH . I 7 HOH C 21 321 46 HOH HOH . I 7 HOH C 22 322 38 HOH HOH . I 7 HOH C 23 323 47 HOH HOH . I 7 HOH C 24 324 42 HOH HOH . I 7 HOH C 25 325 32 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 O5' THM . . . E 5 -10.641 6.37 -14.734 1 70.7 ? O5' THM 101 B 1 HETATM 2 C C5' THM . . . E 5 -10.957 5.359 -15.683 1 71.13 ? C5' THM 101 B 1 HETATM 3 C C4' THM . . . E 5 -10.587 3.99 -15.168 1 63.56 ? C4' THM 101 B 1 HETATM 4 O O4' THM . . . E 5 -9.153 3.906 -14.981 1 62.65 ? O4' THM 101 B 1 HETATM 5 C C3' THM . . . E 5 -11.221 3.648 -13.824 1 61.35 ? C3' THM 101 B 1 HETATM 6 O O3' THM . . . E 5 -11.649 2.292 -13.825 1 63.83 ? O3' THM 101 B 1 HETATM 7 C C2' THM . . . E 5 -10.084 3.879 -12.842 1 63.36 ? C2' THM 101 B 1 HETATM 8 C C1' THM . . . E 5 -8.873 3.466 -13.657 1 63.12 ? C1' THM 101 B 1 HETATM 9 N N1 THM . . . E 5 -7.614 4.107 -13.216 1 60.9 ? N1 THM 101 B 1 HETATM 10 C C2 THM . . . E 5 -6.503 3.314 -13.015 1 53.71 ? C2 THM 101 B 1 HETATM 11 O O2 THM . . . E 5 -6.516 2.099 -13.164 1 53.49 ? O2 THM 101 B 1 HETATM 12 N N3 THM . . . E 5 -5.38 3.991 -12.608 1 57.94 ? N3 THM 101 B 1 HETATM 13 C C4 THM . . . E 5 -5.255 5.353 -12.401 1 59.7 ? C4 THM 101 B 1 HETATM 14 O O4 THM . . . E 5 -4.173 5.822 -12.04 1 60.59 ? O4 THM 101 B 1 HETATM 15 C C5 THM . . . E 5 -6.455 6.125 -12.641 1 55.91 ? C5 THM 101 B 1 HETATM 16 C C5M THM . . . E 5 -6.412 7.609 -12.435 1 57.09 ? C5M THM 101 B 1 HETATM 17 C C6 THM . . . E 5 -7.561 5.474 -13.031 1 58.73 ? C6 THM 101 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #