data_1JUT # _model_server_result.job_id QiEbK5pg2Y7vGs9sdpFVCQ _model_server_result.datetime_utc '2024-11-23 09:16:27' _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 1jut # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 1JUT # _exptl.entry_id 1JUT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 1JUT _cell.length_a 125.8 _cell.length_b 125.8 _cell.length_c 67.063 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JUT _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 434 n n N1 C6 UMP sing 435 n n N1 C1' UMP sing 436 n n C2 N3 UMP sing 437 n n C2 O2 UMP doub 438 n n N3 C4 UMP sing 439 n n N3 HN3 UMP sing 440 n n C4 C5 UMP sing 441 n n C4 O4 UMP doub 442 n n C5 C6 UMP doub 443 n n C5 H5 UMP sing 444 n n C6 H6 UMP sing 445 n n C1' C2' UMP sing 446 n n C1' O4' UMP sing 447 n n C1' H1' UMP sing 448 n n C2' C3' UMP sing 449 n n C2' H2' UMP sing 450 n n C2' "H2''" UMP sing 451 n n C3' C4' UMP sing 452 n n C3' O3' UMP sing 453 n n C3' H3' UMP sing 454 n n C4' O4' UMP sing 455 n n C4' C5' UMP sing 456 n n C4' H4' UMP sing 457 n n O3' HO3' UMP sing 458 n n C5' O5' UMP sing 459 n n C5' H5' UMP sing 460 n n C5' "H5''" UMP sing 461 n n O5' P UMP sing 462 n n P OP1 UMP doub 463 n n P OP2 UMP sing 464 n n P OP3 UMP sing 465 n n OP2 HOP2 UMP sing 466 n n OP3 HOP3 UMP sing 467 n n # _atom_sites.entry_id 1JUT _atom_sites.fract_transf_matrix[1][1] 0.007949 _atom_sites.fract_transf_matrix[1][2] 0.004589 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009179 _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] 0.014911 _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 UMP A 1 302 302 UMP UMP . D 3 LYD A 1 303 303 LYD LYC . E 2 UMP B 1 304 304 UMP UMP . F 3 LYD B 1 305 305 LYD LYC . G 4 HOH A 1 406 406 HOH WAT . G 4 HOH A 2 409 409 HOH WAT . G 4 HOH A 3 410 410 HOH WAT . G 4 HOH A 4 413 413 HOH WAT . G 4 HOH A 5 415 415 HOH WAT . G 4 HOH A 6 417 417 HOH WAT . G 4 HOH A 7 418 418 HOH WAT . G 4 HOH A 8 419 419 HOH WAT . G 4 HOH A 9 422 422 HOH WAT . G 4 HOH A 10 423 423 HOH WAT . G 4 HOH A 11 425 425 HOH WAT . G 4 HOH A 12 426 426 HOH WAT . G 4 HOH A 13 428 428 HOH WAT . G 4 HOH A 14 429 429 HOH WAT . G 4 HOH A 15 430 430 HOH WAT . G 4 HOH A 16 431 431 HOH WAT . G 4 HOH A 17 432 432 HOH WAT . G 4 HOH A 18 433 433 HOH WAT . G 4 HOH A 19 434 434 HOH WAT . G 4 HOH A 20 435 435 HOH WAT . G 4 HOH A 21 436 436 HOH WAT . G 4 HOH A 22 437 437 HOH WAT . G 4 HOH A 23 438 438 HOH WAT . G 4 HOH A 24 439 439 HOH WAT . G 4 HOH A 25 440 440 HOH WAT . G 4 HOH A 26 441 441 HOH WAT . G 4 HOH A 27 442 442 HOH WAT . G 4 HOH A 28 443 443 HOH WAT . G 4 HOH A 29 444 444 HOH WAT . G 4 HOH A 30 445 445 HOH WAT . G 4 HOH A 31 446 446 HOH WAT . G 4 HOH A 32 447 447 HOH WAT . G 4 HOH A 33 448 448 HOH WAT . G 4 HOH A 34 449 449 HOH WAT . G 4 HOH A 35 450 450 HOH WAT . G 4 HOH A 36 451 451 HOH WAT . G 4 HOH A 37 452 452 HOH WAT . G 4 HOH A 38 453 453 HOH WAT . G 4 HOH A 39 454 454 HOH WAT . G 4 HOH A 40 455 455 HOH WAT . G 4 HOH A 41 456 456 HOH WAT . G 4 HOH A 42 457 457 HOH WAT . G 4 HOH A 43 458 458 HOH WAT . G 4 HOH A 44 464 464 HOH WAT . G 4 HOH A 45 473 473 HOH WAT . G 4 HOH A 46 474 474 HOH WAT . G 4 HOH A 47 475 475 HOH WAT . G 4 HOH A 48 477 477 HOH WAT . G 4 HOH A 49 480 480 HOH WAT . H 4 HOH B 1 401 401 HOH WAT . H 4 HOH B 2 402 402 HOH WAT . H 4 HOH B 3 403 403 HOH WAT . H 4 HOH B 4 404 404 HOH WAT . H 4 HOH B 5 405 405 HOH WAT . H 4 HOH B 6 407 407 HOH WAT . H 4 HOH B 7 408 408 HOH WAT . H 4 HOH B 8 411 411 HOH WAT . H 4 HOH B 9 412 412 HOH WAT . H 4 HOH B 10 414 414 HOH WAT . H 4 HOH B 11 416 416 HOH WAT . H 4 HOH B 12 420 420 HOH WAT . H 4 HOH B 13 421 421 HOH WAT . H 4 HOH B 14 424 424 HOH WAT . H 4 HOH B 15 427 427 HOH WAT . H 4 HOH B 16 459 459 HOH WAT . H 4 HOH B 17 460 460 HOH WAT . H 4 HOH B 18 461 461 HOH WAT . H 4 HOH B 19 462 462 HOH WAT . H 4 HOH B 20 463 463 HOH WAT . H 4 HOH B 21 465 465 HOH WAT . H 4 HOH B 22 466 466 HOH WAT . H 4 HOH B 23 467 467 HOH WAT . H 4 HOH B 24 468 468 HOH WAT . H 4 HOH B 25 469 469 HOH WAT . H 4 HOH B 26 470 470 HOH WAT . H 4 HOH B 27 471 471 HOH WAT . H 4 HOH B 28 472 472 HOH WAT . H 4 HOH B 29 476 476 HOH WAT . H 4 HOH B 30 478 478 HOH WAT . H 4 HOH B 31 479 479 HOH WAT . H 4 HOH B 32 481 481 HOH WAT . H 4 HOH B 33 482 482 HOH WAT . # 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 N N1 UMP . . . E 2 43.496 34.026 24.912 1 44.4 ? N1 UMP 304 B 1 HETATM 2 C C2 UMP . . . E 2 42.7 35.017 25.468 1 43.18 ? C2 UMP 304 B 1 HETATM 3 N N3 UMP . . . E 2 41.906 35.778 24.566 1 44.06 ? N3 UMP 304 B 1 HETATM 4 C C4 UMP . . . E 2 41.917 35.617 23.182 1 44.84 ? C4 UMP 304 B 1 HETATM 5 C C5 UMP . . . E 2 42.78 34.572 22.482 1 45 ? C5 UMP 304 B 1 HETATM 6 C C6 UMP . . . E 2 43.624 33.747 23.46 1 44.71 ? C6 UMP 304 B 1 HETATM 7 O O2 UMP . . . E 2 42.504 35.122 26.691 1 40.37 ? O2 UMP 304 B 1 HETATM 8 O O4 UMP . . . E 2 41.098 36.342 22.264 1 46.26 ? O4 UMP 304 B 1 HETATM 9 C C1' UMP . . . E 2 44.761 33.55 25.568 1 44.57 ? C1' UMP 304 B 1 HETATM 10 C C2' UMP . . . E 2 44.45 32.342 26.426 1 43.82 ? C2' UMP 304 B 1 HETATM 11 C C3' UMP . . . E 2 45.847 31.754 26.546 1 43.12 ? C3' UMP 304 B 1 HETATM 12 C C4' UMP . . . E 2 46.377 31.876 25.109 1 43.27 ? C4' UMP 304 B 1 HETATM 13 O O3' UMP . . . E 2 46.603 32.643 27.356 1 42.75 ? O3' UMP 304 B 1 HETATM 14 O O4' UMP . . . E 2 45.706 33.052 24.578 1 44.12 ? O4' UMP 304 B 1 HETATM 15 C C5' UMP . . . E 2 45.927 30.64 24.231 1 43.47 ? C5' UMP 304 B 1 HETATM 16 O O5' UMP . . . E 2 46.651 29.398 24.505 1 42.12 ? O5' UMP 304 B 1 HETATM 17 P P UMP . . . E 2 45.974 27.926 24.663 1 38.2 ? P UMP 304 B 1 HETATM 18 O OP1 UMP . . . E 2 44.929 28.141 25.711 1 38.63 ? OP1 UMP 304 B 1 HETATM 19 O OP2 UMP . . . E 2 45.417 27.517 23.344 1 38.45 ? OP2 UMP 304 B 1 HETATM 20 O OP3 UMP . . . E 2 47.047 26.977 25.103 1 38.85 ? OP3 UMP 304 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #