data_2WTZ # _model_server_result.job_id YOgQ1eqTJVMPGAK4DtYh5Q _model_server_result.datetime_utc '2024-11-27 18:09:05' _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 2wtz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1498}' # _entry.id 2WTZ # _exptl.entry_id 2WTZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 879.608 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 111.09 _cell.angle_beta 92.16 _cell.angle_gamma 93.98 _cell.entry_id 2WTZ _cell.length_a 76.92 _cell.length_b 79.8 _cell.length_c 82.92 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WTZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F 1 1 B,G,H 2 1 C,I,J 3 1 D,K,L 4 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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 ALA 261 A ALA 261 1_555 A N KCX 262 A KCX 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C KCX 262 A KCX 262 1_555 A N ALA 263 A ALA 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C ALA 261 B ALA 261 1_555 B N KCX 262 B KCX 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 B C KCX 262 B KCX 262 1_555 B N ALA 263 B ALA 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale5 C C ALA 261 C ALA 261 1_555 C N KCX 262 C KCX 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 C C KCX 262 C KCX 262 1_555 C N ALA 263 C ALA 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale7 D C ALA 261 D ALA 261 1_555 D N KCX 262 D KCX 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 D C KCX 262 D KCX 262 1_555 D N ALA 263 D ALA 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 248 A HIS 248 1_555 F MG MG . A MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc2 E O21 UAG . A UAG 1498 1_555 F MG MG . A MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc3 B NE2 HIS 248 B HIS 248 1_555 H MG MG . B MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc4 G O21 UAG . B UAG 1498 1_555 H MG MG . B MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc5 C NE2 HIS 248 C HIS 248 1_555 J MG MG . C MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc6 I O21 UAG . C UAG 1498 1_555 J MG MG . C MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 D NE2 HIS 248 D HIS 248 1_555 L MG MG . D MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc8 K O21 UAG . D UAG 1498 1_555 L MG MG . D MG 1499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _chem_comp.formula 'C28 H43 N5 O23 P2' _chem_comp.formula_weight 879.608 _chem_comp.id UAG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE" _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 C6 C5 UAG doub 382 n n C6 N1 UAG sing 383 n n C6 H6 UAG sing 384 n n C5 C4 UAG sing 385 n n C5 H5 UAG sing 386 n n C4 O4 UAG doub 387 n n C4 N3 UAG sing 388 n n N3 C2 UAG sing 389 n n N3 HN3 UAG sing 390 n n C2 O2 UAG doub 391 n n C2 N1 UAG sing 392 n n N1 C1B UAG sing 393 n n C1B C2B UAG sing 394 n n C1B O4B UAG sing 395 n n C1B H1B UAG sing 396 n n C2B O2' UAG sing 397 n n C2B C3B UAG sing 398 n n C2B H2B UAG sing 399 n n O2' "HO'2" UAG sing 400 n n C3B O3B UAG sing 401 n n C3B C4B UAG sing 402 n n C3B H3B UAG sing 403 n n O3B "HO'3" UAG sing 404 n n C4B O4B UAG sing 405 n n C4B C5B UAG sing 406 n n C4B H4B UAG sing 407 n n C5B O5B UAG sing 408 n n C5B "H5'1" UAG sing 409 n n C5B "H5'2" UAG sing 410 n n O5B PA UAG sing 411 n n PA O1A UAG doub 412 n n PA O2A UAG sing 413 n n PA O3A UAG sing 414 n n O2A HOA2 UAG sing 415 n n O3A PB UAG sing 416 n n PB O1B UAG doub 417 n n PB O2B UAG sing 418 n n PB O1' UAG sing 419 n n O2B HOB2 UAG sing 420 n n C1' O1' UAG sing 421 n n C1' C2' UAG sing 422 n n C1' O5' UAG sing 423 n n C1' H1' UAG sing 424 n n C2' N2' UAG sing 425 n n C2' C3' UAG sing 426 n n C2' H2' UAG sing 427 n n N2' C7' UAG sing 428 n n N2' HN2' UAG sing 429 n n C7' O7' UAG doub 430 n n C7' C8' UAG sing 431 n n C8' "H8'1" UAG sing 432 n n C8' "H8'2" UAG sing 433 n n C8' "H8'3" UAG sing 434 n n C3' O3' UAG sing 435 n n C3' C4' UAG sing 436 n n C3' H3' UAG sing 437 n n O3' C18 UAG sing 438 n n C4' O4' UAG sing 439 n n C4' C5' UAG sing 440 n n C4' H4' UAG sing 441 n n O4' HO4' UAG sing 442 n n C5' O5' UAG sing 443 n n C5' C6' UAG sing 444 n n C5' H5' UAG sing 445 n n C6' O6' UAG sing 446 n n C6' "H6'1" UAG sing 447 n n C6' "H6'2" UAG sing 448 n n O6' HO6' UAG sing 449 n n C18 C20 UAG sing 450 n n C18 C19 UAG sing 451 n n C18 H18 UAG sing 452 n n C20 H201 UAG sing 453 n n C20 H202 UAG sing 454 n n C20 H203 UAG sing 455 n n C19 O18 UAG doub 456 n n C19 N4 UAG sing 457 n n N4 C21 UAG sing 458 n n N4 HN4 UAG sing 459 n n C21 C23 UAG sing 460 n n C21 C22 UAG sing 461 n n C21 H21 UAG sing 462 n n C23 H231 UAG sing 463 n n C23 H232 UAG sing 464 n n C23 H233 UAG sing 465 n n C22 O19 UAG doub 466 n n C22 N5 UAG sing 467 n n N5 C24 UAG sing 468 n n N5 HN5 UAG sing 469 n n C24 C25 UAG sing 470 n n C24 C28 UAG sing 471 n n C24 H24 UAG sing 472 n n C25 C26 UAG sing 473 n n C25 H251 UAG sing 474 n n C25 H252 UAG sing 475 n n C26 C27 UAG sing 476 n n C26 H261 UAG sing 477 n n C26 H262 UAG sing 478 n n C27 O20 UAG doub 479 n n C27 O21 UAG sing 480 n n O21 HO1 UAG sing 481 n n C28 O22 UAG doub 482 n n C28 O23 UAG sing 483 n n O23 HO3 UAG sing 484 n n # _atom_sites.entry_id 2WTZ _atom_sites.fract_transf_matrix[1][1] 0.013001 _atom_sites.fract_transf_matrix[1][2] 0.000905 _atom_sites.fract_transf_matrix[1][3] 0.000879 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012562 _atom_sites.fract_transf_matrix[2][3] 0.004903 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012955 _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 E 2 UAG A 1 1498 1498 UAG UAG . F 3 MG A 1 1499 1499 MG MG . G 2 UAG B 1 1498 1498 UAG UAG . H 3 MG B 1 1499 1499 MG MG . I 2 UAG C 1 1498 1498 UAG UAG . J 3 MG C 1 1499 1499 MG MG . K 2 UAG D 1 1498 1498 UAG UAG . L 3 MG D 1 1499 1499 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 C C6 UAG . . . E 2 18.983 1.604 9.863 1 27.85 ? C6 UAG 1498 A 1 HETATM 2 C C5 UAG . . . E 2 18.954 1.132 11.157 1 26.09 ? C5 UAG 1498 A 1 HETATM 3 C C4 UAG . . . E 2 19.489 -0.107 11.421 1 27.64 ? C4 UAG 1498 A 1 HETATM 4 O O4 UAG . . . E 2 19.482 -0.55 12.56 1 26.71 ? O4 UAG 1498 A 1 HETATM 5 N N3 UAG . . . E 2 20.06 -0.875 10.401 1 30.9 ? N3 UAG 1498 A 1 HETATM 6 C C2 UAG . . . E 2 20.084 -0.408 9.09 1 29.75 ? C2 UAG 1498 A 1 HETATM 7 O O2 UAG . . . E 2 20.59 -1.122 8.227 1 31.74 ? O2 UAG 1498 A 1 HETATM 8 N N1 UAG . . . E 2 19.541 0.854 8.816 1 28.24 ? N1 UAG 1498 A 1 HETATM 9 C C1B UAG . . . E 2 19.532 1.401 7.448 1 28.63 ? C1B UAG 1498 A 1 HETATM 10 C C2B UAG . . . E 2 18.053 1.562 7.132 1 28.49 ? C2B UAG 1498 A 1 HETATM 11 O O2' UAG . . . E 2 17.531 0.381 6.554 1 28.9 ? O2' UAG 1498 A 1 HETATM 12 C C3B UAG . . . E 2 18.076 2.636 6.085 1 29.97 ? C3B UAG 1498 A 1 HETATM 13 O O3B UAG . . . E 2 18.418 2.046 4.823 1 29.73 ? O3B UAG 1498 A 1 HETATM 14 C C4B UAG . . . E 2 19.218 3.546 6.568 1 30.77 ? C4B UAG 1498 A 1 HETATM 15 O O4B UAG . . . E 2 20.061 2.731 7.44 1 29.41 ? O4B UAG 1498 A 1 HETATM 16 C C5B UAG . . . E 2 18.774 4.849 7.276 1 32.24 ? C5B UAG 1498 A 1 HETATM 17 O O5B UAG . . . E 2 17.625 4.71 8.114 1 35.47 ? O5B UAG 1498 A 1 HETATM 18 P PA UAG . . . E 2 16.501 5.902 8.37 1 38.84 ? PA UAG 1498 A 1 HETATM 19 O O1A UAG . . . E 2 16.38 4.923 9.699 1 38.64 ? O1A UAG 1498 A 1 HETATM 20 O O2A UAG . . . E 2 17.63 6.896 8.295 1 38.9 ? O2A UAG 1498 A 1 HETATM 21 O O3A UAG . . . E 2 15.898 5.312 6.967 1 38.14 ? O3A UAG 1498 A 1 HETATM 22 P PB UAG . . . E 2 15.001 6.209 5.971 1 39.24 ? PB UAG 1498 A 1 HETATM 23 O O1B UAG . . . E 2 14.747 7.652 6.635 1 40.11 ? O1B UAG 1498 A 1 HETATM 24 O O2B UAG . . . E 2 15.509 6.349 4.57 1 38.75 ? O2B UAG 1498 A 1 HETATM 25 C C1' UAG . . . E 2 12.946 4.737 5.07 1 36.07 ? C1' UAG 1498 A 1 HETATM 26 O O1' UAG . . . E 2 13.55 5.517 6.086 1 37.46 ? O1' UAG 1498 A 1 HETATM 27 C C2' UAG . . . E 2 11.451 4.723 5.384 1 36.33 ? C2' UAG 1498 A 1 HETATM 28 N N2' UAG . . . E 2 11.05 6.096 5.693 1 38.25 ? N2' UAG 1498 A 1 HETATM 29 C C7' UAG . . . E 2 10.467 6.93 4.846 1 40.46 ? C7' UAG 1498 A 1 HETATM 30 O O7' UAG . . . E 2 10.135 6.668 3.689 1 41.54 ? O7' UAG 1498 A 1 HETATM 31 C C8' UAG . . . E 2 10.218 8.307 5.456 1 41.95 ? C8' UAG 1498 A 1 HETATM 32 C C3' UAG . . . E 2 11.171 3.876 6.621 1 34.71 ? C3' UAG 1498 A 1 HETATM 33 O O3' UAG . . . E 2 9.764 3.636 6.661 1 36.29 ? O3' UAG 1498 A 1 HETATM 34 C C4' UAG . . . E 2 11.898 2.541 6.6 1 32.9 ? C4' UAG 1498 A 1 HETATM 35 O O4' UAG . . . E 2 11.827 1.942 7.876 1 31.1 ? O4' UAG 1498 A 1 HETATM 36 C C5' UAG . . . E 2 13.358 2.695 6.249 1 32.25 ? C5' UAG 1498 A 1 HETATM 37 O O5' UAG . . . E 2 13.511 3.402 5.055 1 33.88 ? O5' UAG 1498 A 1 HETATM 38 C C6' UAG . . . E 2 13.887 1.312 5.936 1 33.33 ? C6' UAG 1498 A 1 HETATM 39 O O6' UAG . . . E 2 13.296 0.797 4.738 1 32.78 ? O6' UAG 1498 A 1 HETATM 40 C C18 UAG . . . E 2 9.091 4.312 7.757 1 36.53 ? C18 UAG 1498 A 1 HETATM 41 C C20 UAG . . . E 2 8.636 3.25 8.766 1 35.19 ? C20 UAG 1498 A 1 HETATM 42 C C19 UAG . . . E 2 7.831 5.046 7.281 1 36.47 ? C19 UAG 1498 A 1 HETATM 43 O O18 UAG . . . E 2 7.053 5.486 8.115 1 38.96 ? O18 UAG 1498 A 1 HETATM 44 N N4 UAG . . . E 2 7.591 5.174 5.996 1 35.25 ? N4 UAG 1498 A 1 HETATM 45 C C21 UAG . . . E 2 6.389 5.821 5.505 1 35.45 ? C21 UAG 1498 A 1 HETATM 46 C C23 UAG . . . E 2 6.623 7.31 5.341 1 36.18 ? C23 UAG 1498 A 1 HETATM 47 C C22 UAG . . . E 2 6.028 5.181 4.177 1 37.72 ? C22 UAG 1498 A 1 HETATM 48 O O19 UAG . . . E 2 6.864 4.54 3.541 1 39.36 ? O19 UAG 1498 A 1 HETATM 49 N N5 UAG . . . E 2 4.752 5.353 3.819 1 40.19 ? N5 UAG 1498 A 1 HETATM 50 C C24 UAG . . . E 2 4.072 4.773 2.646 1 41.96 ? C24 UAG 1498 A 1 HETATM 51 C C25 UAG . . . E 2 2.626 4.649 3.081 1 41.85 ? C25 UAG 1498 A 1 HETATM 52 C C26 UAG . . . E 2 1.699 5.721 2.533 1 42.93 ? C26 UAG 1498 A 1 HETATM 53 C C27 UAG . . . E 2 0.262 5.156 2.508 1 42.43 ? C27 UAG 1498 A 1 HETATM 54 O O20 UAG . . . E 2 0.141 3.97 2.901 1 41.33 ? O20 UAG 1498 A 1 HETATM 55 O O21 UAG . . . E 2 -0.663 5.891 2.068 1 40.57 ? O21 UAG 1498 A 1 HETATM 56 C C28 UAG . . . E 2 4.554 3.318 2.315 1 44 ? C28 UAG 1498 A 1 HETATM 57 O O22 UAG . . . E 2 4.689 3.021 1.109 1 45.74 ? O22 UAG 1498 A 1 HETATM 58 O O23 UAG . . . E 2 4.721 2.501 3.257 1 43.81 ? O23 UAG 1498 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 58 #