data_5LKM # _model_server_result.job_id 6bRP1URvaI6xg7Ns87Qd6g _model_server_result.datetime_utc '2025-01-02 16:28:41' _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 5lkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":500}' # _entry.id 5LKM # _exptl.entry_id 5LKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 5LKM _cell.length_a 99.4 _cell.length_b 169.9 _cell.length_c 187.42 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 1,2 # 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' 2_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -99.4 -169.9 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F N N ? 2 H 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 OG SER 102 A SER 102 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc2 D O1B TYD . A TYD 500 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc3 B OG SER 102 B SER 102 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc4 B OE2 GLU 124 B GLU 124 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc5 F O1B TYD . B TYD 500 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? metalc ? metalc6 C OG SER 102 C SER 102 1_555 I MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc7 C OE1 GLU 124 C GLU 124 1_555 I MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc8 H O1B TYD . C TYD 500 1_555 I MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 332 n n PA O2A TYD sing 333 n n PA O3A TYD sing 334 n n PA O5' TYD sing 335 n n O2A HOA2 TYD sing 336 n n O3A PB TYD sing 337 n n PB O1B TYD doub 338 n n PB O2B TYD sing 339 n n PB O3B TYD sing 340 n n O2B HOB2 TYD sing 341 n n O3B HOB3 TYD sing 342 n n O5' C5' TYD sing 343 n n C5' C4' TYD sing 344 n n C5' "H5'1" TYD sing 345 n n C5' "H5'2" TYD sing 346 n n C4' O4' TYD sing 347 n n C4' C3' TYD sing 348 n n C4' H4' TYD sing 349 n n O4' C1' TYD sing 350 n n C3' O3' TYD sing 351 n n C3' C2' TYD sing 352 n n C3' H3' TYD sing 353 n n O3' HO3' TYD sing 354 n n C2' C1' TYD sing 355 n n C2' "H2'1" TYD sing 356 n n C2' "H2'2" TYD sing 357 n n C1' N1 TYD sing 358 n n C1' H1' TYD sing 359 n n N1 C2 TYD sing 360 n y N1 C6 TYD sing 361 n y C2 O2 TYD doub 362 n n C2 N3 TYD sing 363 n y N3 C4 TYD sing 364 n y N3 HN3 TYD sing 365 n n C4 O4 TYD doub 366 n n C4 C5 TYD sing 367 n y C5 C5M TYD sing 368 n n C5 C6 TYD doub 369 n y C5M H51 TYD sing 370 n n C5M H52 TYD sing 371 n n C5M H53 TYD sing 372 n n C6 H6 TYD sing 373 n n # _atom_sites.entry_id 5LKM _atom_sites.fract_transf_matrix[1][1] 0.01006 _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] 0.005886 _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] 0.005336 _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 2 TYD A 1 500 500 TYD TYD . E 3 MG A 1 501 501 MG MG . F 2 TYD B 1 500 500 TYD TYD . G 3 MG B 1 501 501 MG MG . H 2 TYD C 1 500 500 TYD TYD . I 3 MG C 1 501 501 MG MG . # 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 P PA TYD . . . H 2 -49.433 -50.198 -50.554 1 129.06 ? PA TYD 500 C 1 HETATM 2 O O1A TYD . . . H 2 -50.539 -50.125 -51.601 1 125.77 ? O1A TYD 500 C 1 HETATM 3 O O2A TYD . . . H 2 -48.144 -49.504 -50.825 1 120.47 ? O2A TYD 500 C 1 HETATM 4 O O3A TYD . . . H 2 -49.058 -51.723 -50.218 1 126.44 ? O3A TYD 500 C 1 HETATM 5 P PB TYD . . . H 2 -48.401 -52.769 -51.247 1 126.49 ? PB TYD 500 C 1 HETATM 6 O O1B TYD . . . H 2 -48.264 -52.027 -52.558 1 118.83 ? O1B TYD 500 C 1 HETATM 7 O O2B TYD . . . H 2 -47.153 -53.235 -50.545 1 125.95 ? O2B TYD 500 C 1 HETATM 8 O O3B TYD . . . H 2 -49.396 -53.891 -51.253 1 143.93 ? O3B TYD 500 C 1 HETATM 9 O O5' TYD . . . H 2 -49.896 -49.612 -49.114 1 140.1 ? O5' TYD 500 C 1 HETATM 10 C C5' TYD . . . H 2 -50.991 -50.153 -48.388 1 152.01 ? C5' TYD 500 C 1 HETATM 11 C C4' TYD . . . H 2 -52.1 -49.123 -48.287 1 160.65 ? C4' TYD 500 C 1 HETATM 12 O O4' TYD . . . H 2 -51.68 -48.004 -47.498 1 177.93 ? O4' TYD 500 C 1 HETATM 13 C C3' TYD . . . H 2 -52.599 -48.504 -49.602 1 160.98 ? C3' TYD 500 C 1 HETATM 14 O O3' TYD . . . H 2 -53.538 -49.3 -50.32 1 139.05 ? O3' TYD 500 C 1 HETATM 15 C C2' TYD . . . H 2 -53.279 -47.237 -49.13 1 173.66 ? C2' TYD 500 C 1 HETATM 16 C C1' TYD . . . H 2 -52.711 -47.028 -47.716 1 199.61 ? C1' TYD 500 C 1 HETATM 17 N N1 TYD . . . H 2 -52.252 -45.641 -47.56 1 215.47 ? N1 TYD 500 C 1 HETATM 18 C C2 TYD . . . H 2 -52.845 -44.793 -46.587 1 231.6 ? C2 TYD 500 C 1 HETATM 19 O O2 TYD . . . H 2 -53.751 -45.218 -45.832 1 215.96 ? O2 TYD 500 C 1 HETATM 20 N N3 TYD . . . H 2 -52.436 -43.516 -46.453 1 262.09 ? N3 TYD 500 C 1 HETATM 21 C C4 TYD . . . H 2 -51.468 -43.004 -47.234 1 263.72 ? C4 TYD 500 C 1 HETATM 22 O O4 TYD . . . H 2 -51.109 -41.819 -47.101 1 271.78 ? O4 TYD 500 C 1 HETATM 23 C C5 TYD . . . H 2 -50.838 -43.873 -48.262 1 239.27 ? C5 TYD 500 C 1 HETATM 24 C C5M TYD . . . H 2 -49.758 -43.371 -49.173 1 225.9 ? C5M TYD 500 C 1 HETATM 25 C C6 TYD . . . H 2 -51.281 -45.181 -48.362 1 226.64 ? C6 TYD 500 C 1 # _model_server_stats.io_time_ms 131 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #