data_2WTZ
#
_model_server_result.job_id            xfV2DKljqq6vFHQaveOuug 
_model_server_result.datetime_utc      '2024-10-19 17:21:25' 
_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":"I","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 . . . I 2 5.309 36.625 -12.019 1 44.32 ? C6 UAG 1498 C 1 
HETATM 2 C C5 UAG . . . I 2 5.416 37.997 -11.945 1 43.71 ? C5 UAG 1498 C 1 
HETATM 3 C C4 UAG . . . I 2 4.813 38.761 -12.927 1 44.45 ? C4 UAG 1498 C 1 
HETATM 4 O O4 UAG . . . I 2 4.904 39.971 -12.864 1 45.96 ? O4 UAG 1498 C 1 
HETATM 5 N N3 UAG . . . I 2 4.101 38.202 -13.989 1 45.43 ? N3 UAG 1498 C 1 
HETATM 6 C C2 UAG . . . I 2 3.981 36.813 -14.086 1 45.99 ? C2 UAG 1498 C 1 
HETATM 7 O O2 UAG . . . I 2 3.347 36.336 -15.036 1 46.35 ? O2 UAG 1498 C 1 
HETATM 8 N N1 UAG . . . I 2 4.599 36.009 -13.081 1 44.42 ? N1 UAG 1498 C 1 
HETATM 9 C C1B UAG . . . I 2 4.516 34.533 -13.112 1 41.38 ? C1B UAG 1498 C 1 
HETATM 10 C C2B UAG . . . I 2 5.96 34.104 -13.206 1 39.6 ? C2B UAG 1498 C 1 
HETATM 11 O O2' UAG . . . I 2 6.37 34.074 -14.561 1 36.49 ? O2' UAG 1498 C 1 
HETATM 12 C C3B UAG . . . I 2 5.902 32.717 -12.585 1 39.96 ? C3B UAG 1498 C 1 
HETATM 13 O O3B UAG . . . I 2 5.432 31.785 -13.548 1 41.21 ? O3B UAG 1498 C 1 
HETATM 14 C C4B UAG . . . I 2 4.835 32.862 -11.484 1 40.23 ? C4B UAG 1498 C 1 
HETATM 15 O O4B UAG . . . I 2 4.066 34.036 -11.819 1 41.2 ? O4B UAG 1498 C 1 
HETATM 16 C C5B UAG . . . I 2 5.337 33.005 -10.042 1 40.34 ? C5B UAG 1498 C 1 
HETATM 17 O O5B UAG . . . I 2 6.584 33.692 -9.968 1 43.06 ? O5B UAG 1498 C 1 
HETATM 18 P PA UAG . . . I 2 7.789 33.359 -8.882 1 46.4 ? PA UAG 1498 C 1 
HETATM 19 O O1A UAG . . . I 2 8.016 34.923 -9.227 1 46.42 ? O1A UAG 1498 C 1 
HETATM 20 O O2A UAG . . . I 2 6.704 32.945 -7.919 1 45.75 ? O2A UAG 1498 C 1 
HETATM 21 O O3A UAG . . . I 2 8.262 32.304 -10.075 1 44.64 ? O3A UAG 1498 C 1 
HETATM 22 P PB UAG . . . I 2 9.065 30.955 -9.709 1 44.11 ? PB UAG 1498 C 1 
HETATM 23 O O1B UAG . . . I 2 9.354 30.944 -8.12 1 45.31 ? O1B UAG 1498 C 1 
HETATM 24 O O2B UAG . . . I 2 8.394 29.689 -10.107 1 44.87 ? O2B UAG 1498 C 1 
HETATM 25 C C1' UAG . . . I 2 10.963 30.517 -11.523 1 41.87 ? C1' UAG 1498 C 1 
HETATM 26 O O1' UAG . . . I 2 10.506 31.17 -10.369 1 42.37 ? O1' UAG 1498 C 1 
HETATM 27 C C2' UAG . . . I 2 12.471 30.732 -11.558 1 42.55 ? C2' UAG 1498 C 1 
HETATM 28 N N2' UAG . . . I 2 13.002 30.45 -10.238 1 45.74 ? N2' UAG 1498 C 1 
HETATM 29 C C7' UAG . . . I 2 13.576 29.316 -9.874 1 48.51 ? C7' UAG 1498 C 1 
HETATM 30 O O7' UAG . . . I 2 13.754 28.327 -10.605 1 48.9 ? O7' UAG 1498 C 1 
HETATM 31 C C8' UAG . . . I 2 14.025 29.36 -8.4 1 49.56 ? C8' UAG 1498 C 1 
HETATM 32 C C3' UAG . . . I 2 12.839 32.177 -11.852 1 41.3 ? C3' UAG 1498 C 1 
HETATM 33 O O3' UAG . . . I 2 14.239 32.192 -12.088 1 41.52 ? O3' UAG 1498 C 1 
HETATM 34 C C4' UAG . . . I 2 12.107 32.721 -13.068 1 40.76 ? C4' UAG 1498 C 1 
HETATM 35 O O4' UAG . . . I 2 12.29 34.134 -13.093 1 41.51 ? O4' UAG 1498 C 1 
HETATM 36 C C5' UAG . . . I 2 10.623 32.431 -12.956 1 41.02 ? C5' UAG 1498 C 1 
HETATM 37 O O5' UAG . . . I 2 10.37 31.058 -12.72 1 41.79 ? O5' UAG 1498 C 1 
HETATM 38 C C6' UAG . . . I 2 9.949 32.721 -14.265 1 40.69 ? C6' UAG 1498 C 1 
HETATM 39 O O6' UAG . . . I 2 10.379 31.742 -15.187 1 40.86 ? O6' UAG 1498 C 1 
HETATM 40 C C18 UAG . . . I 2 14.998 32.93 -11.109 1 41.57 ? C18 UAG 1498 C 1 
HETATM 41 C C20 UAG . . . I 2 15.478 34.245 -11.74 1 42.22 ? C20 UAG 1498 C 1 
HETATM 42 C C19 UAG . . . I 2 16.259 32.155 -10.742 1 41.3 ? C19 UAG 1498 C 1 
HETATM 43 O O18 UAG . . . I 2 17.125 32.725 -10.088 1 39.39 ? O18 UAG 1498 C 1 
HETATM 44 N N4 UAG . . . I 2 16.385 30.903 -11.169 1 43.02 ? N4 UAG 1498 C 1 
HETATM 45 C C21 UAG . . . I 2 17.587 30.083 -10.924 1 43.35 ? C21 UAG 1498 C 1 
HETATM 46 C C23 UAG . . . I 2 17.444 29.359 -9.585 1 45.96 ? C23 UAG 1498 C 1 
HETATM 47 C C22 UAG . . . I 2 17.777 29.086 -12.084 1 43.01 ? C22 UAG 1498 C 1 
HETATM 48 O O19 UAG . . . I 2 16.84 28.794 -12.829 1 41.66 ? O19 UAG 1498 C 1 
HETATM 49 N N5 UAG . . . I 2 19.021 28.608 -12.19 1 44.22 ? N5 UAG 1498 C 1 
HETATM 50 C C24 UAG . . . I 2 19.542 27.675 -13.231 1 44.1 ? C24 UAG 1498 C 1 
HETATM 51 C C25 UAG . . . I 2 21.023 27.965 -13.352 1 42.48 ? C25 UAG 1498 C 1 
HETATM 52 C C26 UAG . . . I 2 21.896 26.991 -12.615 1 42.6 ? C26 UAG 1498 C 1 
HETATM 53 C C27 UAG . . . I 2 23.283 27.108 -13.208 1 43.21 ? C27 UAG 1498 C 1 
HETATM 54 O O20 UAG . . . I 2 23.425 27.998 -14.07 1 42.99 ? O20 UAG 1498 C 1 
HETATM 55 O O21 UAG . . . I 2 24.157 26.293 -12.82 1 42.38 ? O21 UAG 1498 C 1 
HETATM 56 C C28 UAG . . . I 2 18.972 27.97 -14.627 1 43.95 ? C28 UAG 1498 C 1 
HETATM 57 O O22 UAG . . . I 2 18.679 27 -15.348 1 43.77 ? O22 UAG 1498 C 1 
HETATM 58 O O23 UAG . . . I 2 18.886 29.168 -14.963 1 44.91 ? O23 UAG 1498 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           58 
#