data_2PAR # _model_server_result.job_id e4W2gy_xEaoxF1Ul0bRKDw _model_server_result.datetime_utc '2024-11-20 01:34:20' _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 2par # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 2PAR # _exptl.entry_id 2PAR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-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 120 _cell.entry_id 2PAR _cell.length_a 136.136 _cell.length_b 136.136 _cell.length_c 55.418 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PAR _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PQS hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,B,C,D,E,F,G,H,I 2 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 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 ? 3 D N N ? 3 G 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 35 A HIS 33 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc2 A NE2 HIS 70 A HIS 68 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 A OD2 ASP 71 A ASP 69 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc4 A OD1 ASP 139 A ASP 137 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 C CO CO . A CO 201 1_555 D O3P TMP . A TMP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc6 C CO CO . A CO 201 1_555 H O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc7 B NE2 HIS 35 B HIS 33 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc8 B NE2 HIS 70 B HIS 68 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc9 B OD2 ASP 71 B ASP 69 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc10 B OD1 ASP 139 B ASP 137 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc11 F CO CO . B CO 201 1_555 G O1P TMP . B TMP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc12 F CO CO . B CO 201 1_555 I O HOH . B HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 322 n n P O2P TMP sing 323 n n P O3P TMP sing 324 n n P O5' TMP sing 325 n n O2P HOP2 TMP sing 326 n n O3P HOP3 TMP sing 327 n n O5' C5' TMP sing 328 n n C5' C4' TMP sing 329 n n C5' "H5'1" TMP sing 330 n n C5' "H5'2" TMP sing 331 n n C4' O4' TMP sing 332 n n C4' C3' TMP sing 333 n n C4' H4' TMP sing 334 n n O4' C1' TMP sing 335 n n C3' O3' TMP sing 336 n n C3' C2' TMP sing 337 n n C3' H3' TMP sing 338 n n O3' HO3' TMP sing 339 n n C2' C1' TMP sing 340 n n C2' "H2'1" TMP sing 341 n n C2' "H2'2" TMP sing 342 n n C1' N1 TMP sing 343 n n C1' H1' TMP sing 344 n n N1 C2 TMP sing 345 n n N1 C6 TMP sing 346 n n C2 O2 TMP doub 347 n n C2 N3 TMP sing 348 n n N3 C4 TMP sing 349 n n N3 HN3 TMP sing 350 n n C4 O4 TMP doub 351 n n C4 C5 TMP sing 352 n n C5 C5M TMP sing 353 n n C5 C6 TMP doub 354 n n C5M H51 TMP sing 355 n n C5M H52 TMP sing 356 n n C5M H53 TMP sing 357 n n C6 H6 TMP sing 358 n n # _atom_sites.entry_id 2PAR _atom_sites.fract_transf_matrix[1][1] 0.00735 _atom_sites.fract_transf_matrix[1][2] 0.00424 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00848 _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] 0.01805 _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 CO A 1 201 201 CO CO . D 3 TMP A 1 301 301 TMP TMP . E 4 PEG A 1 401 401 PEG PEG . F 2 CO B 1 201 201 CO CO . G 3 TMP B 1 301 301 TMP TMP . H 5 HOH A 1 402 6 HOH HOH . H 5 HOH A 2 403 7 HOH HOH . H 5 HOH A 3 404 8 HOH HOH . H 5 HOH A 4 405 10 HOH HOH . H 5 HOH A 5 406 11 HOH HOH . H 5 HOH A 6 407 14 HOH HOH . H 5 HOH A 7 408 17 HOH HOH . H 5 HOH A 8 409 18 HOH HOH . H 5 HOH A 9 410 19 HOH HOH . H 5 HOH A 10 411 22 HOH HOH . H 5 HOH A 11 412 26 HOH HOH . H 5 HOH A 12 413 33 HOH HOH . H 5 HOH A 13 414 35 HOH HOH . H 5 HOH A 14 415 40 HOH HOH . H 5 HOH A 15 416 41 HOH HOH . H 5 HOH A 16 417 42 HOH HOH . H 5 HOH A 17 418 43 HOH HOH . H 5 HOH A 18 419 44 HOH HOH . H 5 HOH A 19 420 45 HOH HOH . H 5 HOH A 20 421 46 HOH HOH . H 5 HOH A 21 422 47 HOH HOH . H 5 HOH A 22 423 52 HOH HOH . H 5 HOH A 23 424 54 HOH HOH . H 5 HOH A 24 425 57 HOH HOH . I 5 HOH B 1 302 1 HOH HOH . I 5 HOH B 2 303 2 HOH HOH . I 5 HOH B 3 304 3 HOH HOH . I 5 HOH B 4 305 4 HOH HOH . I 5 HOH B 5 306 9 HOH HOH . I 5 HOH B 6 307 12 HOH HOH . I 5 HOH B 7 308 13 HOH HOH . I 5 HOH B 8 309 16 HOH HOH . I 5 HOH B 9 310 20 HOH HOH . I 5 HOH B 10 311 23 HOH HOH . I 5 HOH B 11 312 24 HOH HOH . I 5 HOH B 12 313 29 HOH HOH . I 5 HOH B 13 314 31 HOH HOH . I 5 HOH B 14 315 32 HOH HOH . I 5 HOH B 15 316 48 HOH HOH . I 5 HOH B 16 317 53 HOH HOH . I 5 HOH B 17 318 55 HOH HOH . I 5 HOH B 18 319 58 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 P P TMP . . . D 3 -21.522 -8.393 6.739 1 44.21 ? P TMP 301 A 1 HETATM 2 O O1P TMP . . . D 3 -22.931 -8.264 6.147 1 40.7 ? O1P TMP 301 A 1 HETATM 3 O O2P TMP . . . D 3 -21.439 -8.677 8.276 1 42.94 ? O2P TMP 301 A 1 HETATM 4 O O3P TMP . . . D 3 -20.671 -9.368 5.967 1 37.82 ? O3P TMP 301 A 1 HETATM 5 O O5' TMP . . . D 3 -20.774 -6.941 6.632 1 41.49 ? O5' TMP 301 A 1 HETATM 6 C C5' TMP . . . D 3 -21.173 -5.843 5.804 1 41.87 ? C5' TMP 301 A 1 HETATM 7 C C4' TMP . . . D 3 -20.346 -4.574 6.11 1 39.64 ? C4' TMP 301 A 1 HETATM 8 O O4' TMP . . . D 3 -20.727 -4.148 7.41 1 42.04 ? O4' TMP 301 A 1 HETATM 9 C C3' TMP . . . D 3 -18.833 -4.744 6.174 1 39.68 ? C3' TMP 301 A 1 HETATM 10 O O3' TMP . . . D 3 -18.124 -3.597 5.703 1 34.68 ? O3' TMP 301 A 1 HETATM 11 C C2' TMP . . . D 3 -18.47 -4.853 7.653 1 42.11 ? C2' TMP 301 A 1 HETATM 12 C C1' TMP . . . D 3 -19.58 -4.037 8.29 1 45.05 ? C1' TMP 301 A 1 HETATM 13 N N1 TMP . . . D 3 -20.017 -4.5 9.617 1 46.74 ? N1 TMP 301 A 1 HETATM 14 C C2 TMP . . . D 3 -20.081 -3.544 10.676 1 47.27 ? C2 TMP 301 A 1 HETATM 15 O O2 TMP . . . D 3 -19.697 -2.35 10.497 1 48.34 ? O2 TMP 301 A 1 HETATM 16 N N3 TMP . . . D 3 -20.526 -3.901 11.889 1 47.52 ? N3 TMP 301 A 1 HETATM 17 C C4 TMP . . . D 3 -20.932 -5.154 12.121 1 47.63 ? C4 TMP 301 A 1 HETATM 18 O O4 TMP . . . D 3 -21.302 -5.485 13.256 1 47.02 ? O4 TMP 301 A 1 HETATM 19 C C5 TMP . . . D 3 -20.906 -6.169 11.035 1 46.58 ? C5 TMP 301 A 1 HETATM 20 C C5M TMP . . . D 3 -21.377 -7.593 11.31 1 47.88 ? C5M TMP 301 A 1 HETATM 21 C C6 TMP . . . D 3 -20.434 -5.77 9.798 1 46.01 ? C6 TMP 301 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #