data_2J9R # _model_server_result.job_id u6yVULmWqFoR1td_P1F3Sg _model_server_result.datetime_utc '2025-09-12 17:28:33' _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 2j9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1195}' # _entry.id 2J9R # _exptl.entry_id 2J9R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _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 2J9R _cell.length_a 73.171 _cell.length_b 73.171 _cell.length_c 223.734 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J9R _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 15_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -73.171 73.171 0 4 'crystal symmetry operation' 10_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -73.171 73.171 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 SG CYS 165 A CYS 145 1_555 B ZN ZN . A ZN 1194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc2 A SG CYS 168 A CYS 148 1_555 B ZN ZN . A ZN 1194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc3 A SG CYS 203 A CYS 183 1_555 B ZN ZN . A ZN 1194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc4 A SG CYS 206 A CYS 186 1_555 B ZN ZN . A ZN 1194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 294 n n O5' HO5' THM sing 295 n n C5' C4' THM sing 296 n n C5' "H5'1" THM sing 297 n n C5' "H5'2" THM sing 298 n n C4' O4' THM sing 299 n n C4' C3' THM sing 300 n n C4' H4' THM sing 301 n n O4' C1' THM sing 302 n n C3' O3' THM sing 303 n n C3' C2' THM sing 304 n n C3' H3' THM sing 305 n n O3' HO3' THM sing 306 n n C2' C1' THM sing 307 n n C2' "H2'1" THM sing 308 n n C2' "H2'2" THM sing 309 n n C1' N1 THM sing 310 n n C1' H1' THM sing 311 n n N1 C2 THM sing 312 n n N1 C6 THM sing 313 n n C2 O2 THM doub 314 n n C2 N3 THM sing 315 n n N3 C4 THM sing 316 n n N3 HN3 THM sing 317 n n C4 O4 THM doub 318 n n C4 C5 THM sing 319 n n C5 C5M THM sing 320 n n C5 C6 THM doub 321 n n C5M HM51 THM sing 322 n n C5M HM52 THM sing 323 n n C5M HM53 THM sing 324 n n C6 H6 THM sing 325 n n # _atom_sites.entry_id 2J9R _atom_sites.fract_transf_matrix[1][1] 0.013667 _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] 0.013667 _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] 0.00447 _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 ZN A 1 1194 1194 ZN ZN . C 3 THM A 1 1195 1195 THM THM . D 4 PO4 A 1 1196 1196 PO4 PO4 . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 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 . . . C 3 -38.327 13.573 5.104 1 44.46 ? O5' THM 1195 A 1 HETATM 2 C C5' THM . . . C 3 -36.987 13.5 5.603 1 45.3 ? C5' THM 1195 A 1 HETATM 3 C C4' THM . . . C 3 -36.534 12.04 5.647 1 46.88 ? C4' THM 1195 A 1 HETATM 4 O O4' THM . . . C 3 -35.137 11.96 5.95 1 46.73 ? O4' THM 1195 A 1 HETATM 5 C C3' THM . . . C 3 -37.245 11.204 6.703 1 47.48 ? C3' THM 1195 A 1 HETATM 6 O O3' THM . . . C 3 -37.629 9.95 6.126 1 49.97 ? O3' THM 1195 A 1 HETATM 7 C C2' THM . . . C 3 -36.218 10.934 7.783 1 46.74 ? C2' THM 1195 A 1 HETATM 8 C C1' THM . . . C 3 -34.888 11.096 7.068 1 44.7 ? C1' THM 1195 A 1 HETATM 9 N N1 THM . . . C 3 -33.819 11.686 7.897 1 44.14 ? N1 THM 1195 A 1 HETATM 10 C C2 THM . . . C 3 -32.585 10.996 7.978 1 43.8 ? C2 THM 1195 A 1 HETATM 11 O O2 THM . . . C 3 -32.462 9.905 7.369 1 43.65 ? O2 THM 1195 A 1 HETATM 12 N N3 THM . . . C 3 -31.554 11.478 8.697 1 43.15 ? N3 THM 1195 A 1 HETATM 13 C C4 THM . . . C 3 -31.666 12.643 9.349 1 43.25 ? C4 THM 1195 A 1 HETATM 14 O O4 THM . . . C 3 -30.71 13.101 10.012 1 43.33 ? O4 THM 1195 A 1 HETATM 15 C C5 THM . . . C 3 -32.935 13.392 9.273 1 42.92 ? C5 THM 1195 A 1 HETATM 16 C C5M THM . . . C 3 -33.072 14.702 9.994 1 43.58 ? C5M THM 1195 A 1 HETATM 17 C C6 THM . . . C 3 -33.981 12.866 8.524 1 43.64 ? C6 THM 1195 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #