data_4GZ5
#
_model_server_result.job_id            dXAzb-plFdVYTn2ab7y5Hw 
_model_server_result.datetime_utc      '2024-11-27 12:11:35' 
_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          4gz5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1501}' 
#
_entry.id    4GZ5 
#
_exptl.entry_id    4GZ5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              607.354 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE 
_entity.pdbx_number_of_molecules    4 
_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            4GZ5 
_cell.length_a            272.039 
_cell.length_b            272.039 
_cell.length_c            142.08 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GZ5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA dodecameric 12 author_and_software_defined_assembly 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,I,Y 1 1 
B,J,K,L,M,N,Z 2 1 
C,O,P,Q,R,S 3 1 
D,T,U,V,W,X,AA 4 1 
D,T,U,V,W,X,AA 5 2,3,4 
A,B,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,Y,Z 5 1,5,6 
#
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' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0 0 -142.08 
3 'crystal symmetry operation' 2_564 -y,x-y+1,z-1 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.0195 235.592685 -142.08 
4 'crystal symmetry operation' 3_454 -x+y-1,-x,z-1 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.039 0 -142.08 
5 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.0195 235.592685 0 
6 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.039 0 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 J N N 
? 2 O N N 
? 2 T N N 
#
_chem_comp.formula           'C17 H27 N3 O17 P2' 
_chem_comp.formula_weight    607.354 
_chem_comp.id                UD1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE 
_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
C1' C2' UD1 sing 362 n n 
C1' O1' UD1 sing 363 n n 
C1' O5' UD1 sing 364 n n 
C1' H1' UD1 sing 365 n n 
C2' C3' UD1 sing 366 n n 
C2' N2' UD1 sing 367 n n 
C2' H2' UD1 sing 368 n n 
C3' C4' UD1 sing 369 n n 
C3' O3' UD1 sing 370 n n 
C3' H3' UD1 sing 371 n n 
C4' C5' UD1 sing 372 n n 
C4' O4' UD1 sing 373 n n 
C4' H4' UD1 sing 374 n n 
C5' C6' UD1 sing 375 n n 
C5' O5' UD1 sing 376 n n 
C5' H5' UD1 sing 377 n n 
C6' O6' UD1 sing 378 n n 
C6' "H6'1" UD1 sing 379 n n 
C6' "H6'2" UD1 sing 380 n n 
C7' C8' UD1 sing 381 n n 
C7' N2' UD1 sing 382 n n 
C7' O7' UD1 doub 383 n n 
C8' "H8'1" UD1 sing 384 n n 
C8' "H8'2" UD1 sing 385 n n 
C8' "H8'3" UD1 sing 386 n n 
N2' HN2' UD1 sing 387 n n 
O1' PB UD1 sing 388 n n 
O3' HO3' UD1 sing 389 n n 
O4' HO4' UD1 sing 390 n n 
O6' HO6' UD1 sing 391 n n 
N1 C2 UD1 sing 392 n n 
N1 C6 UD1 sing 393 n n 
N1 C1B UD1 sing 394 n n 
C2 N3 UD1 sing 395 n n 
C2 O2 UD1 doub 396 n n 
N3 C4 UD1 sing 397 n n 
N3 HN3 UD1 sing 398 n n 
C4 C5 UD1 sing 399 n n 
C4 O4 UD1 doub 400 n n 
C5 C6 UD1 doub 401 n n 
C5 H5 UD1 sing 402 n n 
C6 H6 UD1 sing 403 n n 
C1B C2B UD1 sing 404 n n 
C1B O4B UD1 sing 405 n n 
C1B H1B UD1 sing 406 n n 
C2B O2' UD1 sing 407 n n 
C2B C3B UD1 sing 408 n n 
C2B H2B UD1 sing 409 n n 
O2' HO2' UD1 sing 410 n n 
C3B C4B UD1 sing 411 n n 
C3B O3B UD1 sing 412 n n 
C3B H3B UD1 sing 413 n n 
C4B O4B UD1 sing 414 n n 
C4B C5B UD1 sing 415 n n 
C4B H4B UD1 sing 416 n n 
O3B HO3A UD1 sing 417 n n 
C5B O5B UD1 sing 418 n n 
C5B "H5'1" UD1 sing 419 n n 
C5B "H5'2" UD1 sing 420 n n 
O5B PA UD1 sing 421 n n 
PA O1A UD1 doub 422 n n 
PA O2A UD1 sing 423 n n 
PA O3A UD1 sing 424 n n 
O2A HOA2 UD1 sing 425 n n 
O3A PB UD1 sing 426 n n 
PB O1B UD1 doub 427 n n 
PB O2B UD1 sing 428 n n 
O2B HOB2 UD1 sing 429 n n 
#
_atom_sites.entry_id                     4GZ5 
_atom_sites.fract_transf_matrix[1][1]    0.003676 
_atom_sites.fract_transf_matrix[1][2]    0.002122 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004245 
_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]    0.007038 
_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 UD1 A 1 1501 1501 UD1 UD1 . 
F 3 SO4 A 1 1502 1601 SO4 SO4 . 
G 3 SO4 A 1 1503 1602 SO4 SO4 . 
H 3 SO4 A 1 1504 1603 SO4 SO4 . 
I 3 SO4 A 1 1505 1604 SO4 SO4 . 
J 2 UD1 B 1 1501 1501 UD1 UD1 . 
K 3 SO4 B 1 1502 1601 SO4 SO4 . 
L 3 SO4 B 1 1503 1602 SO4 SO4 . 
M 3 SO4 B 1 1504 1603 SO4 SO4 . 
N 3 SO4 B 1 1505 1604 SO4 SO4 . 
O 2 UD1 C 1 1501 1501 UD1 UD1 . 
P 3 SO4 C 1 1502 1601 SO4 SO4 . 
Q 3 SO4 C 1 1503 1602 SO4 SO4 . 
R 3 SO4 C 1 1504 1603 SO4 SO4 . 
S 3 SO4 C 1 1505 1604 SO4 SO4 . 
T 2 UD1 D 1 1501 1501 UD1 UD1 . 
U 3 SO4 D 1 1502 1601 SO4 SO4 . 
V 3 SO4 D 1 1503 1602 SO4 SO4 . 
W 3 SO4 D 1 1504 1603 SO4 SO4 . 
X 3 SO4 D 1 1505 1604 SO4 SO4 . 
Y 4 HOH A 1 1601 4 HOH HOH . 
Y 4 HOH A 2 1602 8 HOH HOH . 
Y 4 HOH A 3 1603 9 HOH HOH . 
Z 4 HOH B 1 1601 3 HOH HOH . 
Z 4 HOH B 2 1602 10 HOH HOH . 
Z 4 HOH B 3 1603 12 HOH HOH . 
Z 4 HOH B 4 1604 16 HOH HOH . 
Z 4 HOH B 5 1605 17 HOH HOH . 
Z 4 HOH B 6 1606 18 HOH HOH . 
AA 4 HOH D 1 1601 1 HOH HOH . 
AA 4 HOH D 2 1602 2 HOH HOH . 
AA 4 HOH D 3 1603 7 HOH HOH . 
AA 4 HOH D 4 1604 11 HOH HOH . 
AA 4 HOH D 5 1605 13 HOH HOH . 
AA 4 HOH D 6 1606 14 HOH HOH . 
AA 4 HOH D 7 1607 15 HOH HOH . 
AA 4 HOH D 8 1608 19 HOH HOH . 
AA 4 HOH D 9 1609 20 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 C C1' UD1 . . . J 2 -105.51 21.673 -24.33 1 76.65 ? C1' UD1 1501 B 1 
HETATM 2 C C2' UD1 . . . J 2 -106.527 20.503 -24.038 1 81.34 ? C2' UD1 1501 B 1 
HETATM 3 C C3' UD1 . . . J 2 -107.087 19.94 -25.357 1 80.96 ? C3' UD1 1501 B 1 
HETATM 4 C C4' UD1 . . . J 2 -107.695 21.088 -26.199 1 79.29 ? C4' UD1 1501 B 1 
HETATM 5 C C5' UD1 . . . J 2 -106.681 22.264 -26.328 1 78.55 ? C5' UD1 1501 B 1 
HETATM 6 C C6' UD1 . . . J 2 -107.346 23.488 -26.946 1 78.63 ? C6' UD1 1501 B 1 
HETATM 7 C C7' UD1 . . . J 2 -106.071 19.242 -21.967 1 80.16 ? C7' UD1 1501 B 1 
HETATM 8 C C8' UD1 . . . J 2 -105.231 18.152 -21.367 1 79.64 ? C8' UD1 1501 B 1 
HETATM 9 N N2' UD1 . . . J 2 -105.825 19.486 -23.283 1 81.13 ? N2' UD1 1501 B 1 
HETATM 10 O O1' UD1 . . . J 2 -104.455 21.239 -25.067 1 76 ? O1' UD1 1501 B 1 
HETATM 11 O O3' UD1 . . . J 2 -108.112 19.041 -25.063 1 81.46 ? O3' UD1 1501 B 1 
HETATM 12 O O4' UD1 . . . J 2 -108.003 20.538 -27.455 1 77.89 ? O4' UD1 1501 B 1 
HETATM 13 O O5' UD1 . . . J 2 -106.21 22.657 -25.059 1 77.79 ? O5' UD1 1501 B 1 
HETATM 14 O O6' UD1 . . . J 2 -108.463 23.838 -26.18 1 78.55 ? O6' UD1 1501 B 1 
HETATM 15 O O7' UD1 . . . J 2 -106.909 19.853 -21.306 1 79.54 ? O7' UD1 1501 B 1 
HETATM 16 N N1 UD1 . . . J 2 -97.215 27.214 -25.656 1 47.17 ? N1 UD1 1501 B 1 
HETATM 17 C C2 UD1 . . . J 2 -96.557 28.491 -25.84 1 47.87 ? C2 UD1 1501 B 1 
HETATM 18 N N3 UD1 . . . J 2 -95.207 28.611 -25.445 1 47.75 ? N3 UD1 1501 B 1 
HETATM 19 C C4 UD1 . . . J 2 -94.585 27.517 -25.044 1 47.89 ? C4 UD1 1501 B 1 
HETATM 20 C C5 UD1 . . . J 2 -95.214 26.269 -24.748 1 48.26 ? C5 UD1 1501 B 1 
HETATM 21 C C6 UD1 . . . J 2 -96.537 26.172 -25.087 1 48.16 ? C6 UD1 1501 B 1 
HETATM 22 O O2 UD1 . . . J 2 -97.143 29.433 -26.32 1 49.06 ? O2 UD1 1501 B 1 
HETATM 23 O O4 UD1 . . . J 2 -93.283 27.633 -24.718 1 48.01 ? O4 UD1 1501 B 1 
HETATM 24 C C1B UD1 . . . J 2 -98.638 27.042 -26.059 1 46.02 ? C1B UD1 1501 B 1 
HETATM 25 C C2B UD1 . . . J 2 -98.859 25.944 -27.115 1 46.46 ? C2B UD1 1501 B 1 
HETATM 26 O O2' UD1 . . . J 2 -98.483 26.465 -28.346 1 47.16 ? O2' UD1 1501 B 1 
HETATM 27 C C3B UD1 . . . J 2 -100.368 25.688 -26.902 1 46.64 ? C3B UD1 1501 B 1 
HETATM 28 C C4B UD1 . . . J 2 -100.554 25.966 -25.392 1 46.07 ? C4B UD1 1501 B 1 
HETATM 29 O O4B UD1 . . . J 2 -99.375 26.663 -24.964 1 45.66 ? O4B UD1 1501 B 1 
HETATM 30 O O3B UD1 . . . J 2 -101.03 26.61 -27.704 1 47.38 ? O3B UD1 1501 B 1 
HETATM 31 C C5B UD1 . . . J 2 -100.64 24.713 -24.496 1 46.41 ? C5B UD1 1501 B 1 
HETATM 32 O O5B UD1 . . . J 2 -101.669 24.933 -23.636 1 47.02 ? O5B UD1 1501 B 1 
HETATM 33 P PA UD1 . . . J 2 -102.49 23.544 -22.991 1 59.93 ? PA UD1 1501 B 1 
HETATM 34 O O1A UD1 . . . J 2 -103.836 24.098 -22.684 1 59.85 ? O1A UD1 1501 B 1 
HETATM 35 O O2A UD1 . . . J 2 -101.451 23.121 -21.997 1 59.65 ? O2A UD1 1501 B 1 
HETATM 36 O O3A UD1 . . . J 2 -102.486 22.479 -24.15 1 35.44 ? O3A UD1 1501 B 1 
HETATM 37 P PB UD1 . . . J 2 -102.808 20.987 -24.504 1 63.85 ? PB UD1 1501 B 1 
HETATM 38 O O1B UD1 . . . J 2 -102.977 20.127 -23.301 1 64.55 ? O1B UD1 1501 B 1 
HETATM 39 O O2B UD1 . . . J 2 -102.121 20.487 -25.734 1 63.69 ? O2B UD1 1501 B 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#