data_3PRJ
#
_model_server_result.job_id            iQo5-kAcR-PrwPRrCqY6yg 
_model_server_result.datetime_utc      '2025-07-21 09:00:40' 
_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          3prj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    3PRJ 
#
_exptl.entry_id    3PRJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              536.276 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" 
_entity.pdbx_number_of_molecules    6 
_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         90 
_cell.entry_id            3PRJ 
_cell.length_a            111.79 
_cell.length_b            160.64 
_cell.length_c            205.86 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PRJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 
_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
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R N N 
#
_chem_comp.formula           'C14 H22 N2 O16 P2' 
_chem_comp.formula_weight    536.276 
_chem_comp.id                UDX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     UDP-ALPHA-D-XYLOPYRANOSE 
#
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' UDX sing 435 n n 
C1' O5' UDX sing 436 n n 
C1' O3B UDX sing 437 n n 
C1' H1' UDX sing 438 n n 
C2' O2' UDX sing 439 n n 
C2' C3' UDX sing 440 n n 
C2' "H2'1" UDX sing 441 n n 
O2' "HO'2" UDX sing 442 n n 
C3' O3' UDX sing 443 n n 
C3' C4' UDX sing 444 n n 
C3' "H3'1" UDX sing 445 n n 
O3' "HO'3" UDX sing 446 n n 
C4' O4' UDX sing 447 n n 
C4' C5' UDX sing 448 n n 
C4' "H4'1" UDX sing 449 n n 
O4' "HO'4" UDX sing 450 n n 
C5' O5' UDX sing 451 n n 
C5' "H5'1" UDX sing 452 n n 
C5' "H5'2" UDX sing 453 n n 
PB O1B UDX doub 454 n n 
PB O2B UDX sing 455 n n 
PB O3B UDX sing 456 n n 
PB O3A UDX sing 457 n n 
O2B HOB2 UDX sing 458 n n 
O3A PA UDX sing 459 n n 
PA O1A UDX doub 460 n n 
PA O2A UDX sing 461 n n 
PA O5D UDX sing 462 n n 
O2A HOA2 UDX sing 463 n n 
O5D C5D UDX sing 464 n n 
C5D C4D UDX sing 465 n n 
C5D H5A1 UDX sing 466 n n 
C5D H5A2 UDX sing 467 n n 
C4D O4D UDX sing 468 n n 
C4D C3D UDX sing 469 n n 
C4D H4A1 UDX sing 470 n n 
O4D C1D UDX sing 471 n n 
C3D O3D UDX sing 472 n n 
C3D C2D UDX sing 473 n n 
C3D H3A1 UDX sing 474 n n 
O3D HOA3 UDX sing 475 n n 
C2D O2D UDX sing 476 n n 
C2D C1D UDX sing 477 n n 
C2D H2A1 UDX sing 478 n n 
O2D HOC2 UDX sing 479 n n 
C1D N1 UDX sing 480 n n 
C1D "H1'1" UDX sing 481 n n 
N1 C6 UDX sing 482 n n 
N1 C2 UDX sing 483 n n 
C6 C5 UDX doub 484 n n 
C6 H61 UDX sing 485 n n 
C2 O2 UDX doub 486 n n 
C2 N3 UDX sing 487 n n 
N3 C4 UDX sing 488 n n 
N3 HN3 UDX sing 489 n n 
C4 O4 UDX doub 490 n n 
C4 C5 UDX sing 491 n n 
C5 H51 UDX sing 492 n n 
#
_atom_sites.entry_id                     3PRJ 
_atom_sites.fract_transf_matrix[1][1]    0.008945 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006225 
_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]    0.004858 
_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
G 2 NAI A 1 500 500 NAI NAI . 
H 3 UDX A 1 501 501 UDX UDX . 
I 2 NAI B 1 500 500 NAI NAI . 
J 3 UDX B 1 501 501 UDX UDX . 
K 2 NAI C 1 500 500 NAI NAI . 
L 3 UDX C 1 501 501 UDX UDX . 
M 2 NAI D 1 500 500 NAI NAI . 
N 3 UDX D 1 501 501 UDX UDX . 
O 2 NAI E 1 500 500 NAI NAI . 
P 3 UDX E 1 501 501 UDX UDX . 
Q 2 NAI F 1 500 500 NAI NAI . 
R 3 UDX F 1 501 501 UDX UDX . 
S 4 HOH A 1 495 495 HOH HOH . 
S 4 HOH A 2 496 496 HOH HOH . 
S 4 HOH A 3 497 497 HOH HOH . 
S 4 HOH A 4 498 498 HOH HOH . 
S 4 HOH A 5 499 499 HOH HOH . 
S 4 HOH A 6 502 502 HOH HOH . 
S 4 HOH A 7 503 503 HOH HOH . 
S 4 HOH A 8 504 504 HOH HOH . 
S 4 HOH A 9 505 505 HOH HOH . 
S 4 HOH A 10 506 506 HOH HOH . 
S 4 HOH A 11 507 507 HOH HOH . 
S 4 HOH A 12 508 508 HOH HOH . 
S 4 HOH A 13 509 509 HOH HOH . 
S 4 HOH A 14 510 510 HOH HOH . 
S 4 HOH A 15 511 511 HOH HOH . 
S 4 HOH A 16 512 512 HOH HOH . 
S 4 HOH A 17 513 513 HOH HOH . 
S 4 HOH A 18 514 514 HOH HOH . 
S 4 HOH A 19 515 515 HOH HOH . 
S 4 HOH A 20 516 516 HOH HOH . 
S 4 HOH A 21 517 517 HOH HOH . 
S 4 HOH A 22 518 518 HOH HOH . 
S 4 HOH A 23 519 519 HOH HOH . 
S 4 HOH A 24 520 520 HOH HOH . 
S 4 HOH A 25 521 521 HOH HOH . 
S 4 HOH A 26 522 522 HOH HOH . 
S 4 HOH A 27 523 523 HOH HOH . 
S 4 HOH A 28 524 524 HOH HOH . 
S 4 HOH A 29 525 525 HOH HOH . 
S 4 HOH A 30 526 526 HOH HOH . 
S 4 HOH A 31 527 527 HOH HOH . 
S 4 HOH A 32 528 528 HOH HOH . 
S 4 HOH A 33 529 529 HOH HOH . 
S 4 HOH A 34 530 530 HOH HOH . 
S 4 HOH A 35 531 531 HOH HOH . 
S 4 HOH A 36 532 532 HOH HOH . 
T 4 HOH B 1 495 495 HOH HOH . 
T 4 HOH B 2 496 496 HOH HOH . 
T 4 HOH B 3 497 497 HOH HOH . 
T 4 HOH B 4 498 498 HOH HOH . 
T 4 HOH B 5 499 499 HOH HOH . 
T 4 HOH B 6 502 502 HOH HOH . 
T 4 HOH B 7 503 503 HOH HOH . 
T 4 HOH B 8 504 504 HOH HOH . 
T 4 HOH B 9 505 505 HOH HOH . 
T 4 HOH B 10 506 506 HOH HOH . 
T 4 HOH B 11 507 507 HOH HOH . 
T 4 HOH B 12 508 508 HOH HOH . 
T 4 HOH B 13 509 509 HOH HOH . 
T 4 HOH B 14 510 510 HOH HOH . 
T 4 HOH B 15 511 511 HOH HOH . 
T 4 HOH B 16 512 512 HOH HOH . 
T 4 HOH B 17 513 513 HOH HOH . 
T 4 HOH B 18 514 514 HOH HOH . 
T 4 HOH B 19 515 515 HOH HOH . 
T 4 HOH B 20 516 516 HOH HOH . 
T 4 HOH B 21 517 517 HOH HOH . 
T 4 HOH B 22 518 518 HOH HOH . 
T 4 HOH B 23 519 519 HOH HOH . 
T 4 HOH B 24 520 520 HOH HOH . 
T 4 HOH B 25 521 521 HOH HOH . 
T 4 HOH B 26 522 522 HOH HOH . 
T 4 HOH B 27 523 523 HOH HOH . 
T 4 HOH B 28 524 524 HOH HOH . 
T 4 HOH B 29 525 525 HOH HOH . 
T 4 HOH B 30 526 526 HOH HOH . 
T 4 HOH B 31 527 527 HOH HOH . 
T 4 HOH B 32 528 528 HOH HOH . 
U 4 HOH C 1 495 495 HOH HOH . 
U 4 HOH C 2 496 496 HOH HOH . 
U 4 HOH C 3 497 497 HOH HOH . 
U 4 HOH C 4 498 498 HOH HOH . 
U 4 HOH C 5 499 499 HOH HOH . 
U 4 HOH C 6 502 502 HOH HOH . 
U 4 HOH C 7 503 503 HOH HOH . 
U 4 HOH C 8 504 504 HOH HOH . 
U 4 HOH C 9 505 505 HOH HOH . 
U 4 HOH C 10 506 506 HOH HOH . 
U 4 HOH C 11 507 507 HOH HOH . 
U 4 HOH C 12 508 508 HOH HOH . 
U 4 HOH C 13 509 509 HOH HOH . 
V 4 HOH D 1 495 495 HOH HOH . 
V 4 HOH D 2 496 496 HOH HOH . 
V 4 HOH D 3 497 497 HOH HOH . 
V 4 HOH D 4 498 498 HOH HOH . 
V 4 HOH D 5 499 499 HOH HOH . 
V 4 HOH D 6 502 502 HOH HOH . 
V 4 HOH D 7 503 503 HOH HOH . 
V 4 HOH D 8 504 504 HOH HOH . 
V 4 HOH D 9 505 505 HOH HOH . 
V 4 HOH D 10 506 506 HOH HOH . 
V 4 HOH D 11 507 507 HOH HOH . 
V 4 HOH D 12 508 508 HOH HOH . 
V 4 HOH D 13 509 509 HOH HOH . 
V 4 HOH D 14 510 510 HOH HOH . 
V 4 HOH D 15 511 511 HOH HOH . 
V 4 HOH D 16 512 512 HOH HOH . 
V 4 HOH D 17 513 513 HOH HOH . 
V 4 HOH D 18 514 514 HOH HOH . 
V 4 HOH D 19 515 515 HOH HOH . 
V 4 HOH D 20 516 516 HOH HOH . 
V 4 HOH D 21 517 517 HOH HOH . 
V 4 HOH D 22 518 518 HOH HOH . 
V 4 HOH D 23 519 519 HOH HOH . 
W 4 HOH E 1 495 495 HOH HOH . 
W 4 HOH E 2 496 496 HOH HOH . 
W 4 HOH E 3 497 497 HOH HOH . 
W 4 HOH E 4 498 498 HOH HOH . 
W 4 HOH E 5 499 499 HOH HOH . 
W 4 HOH E 6 502 502 HOH HOH . 
W 4 HOH E 7 503 503 HOH HOH . 
W 4 HOH E 8 504 504 HOH HOH . 
W 4 HOH E 9 505 505 HOH HOH . 
W 4 HOH E 10 506 506 HOH HOH . 
W 4 HOH E 11 507 507 HOH HOH . 
W 4 HOH E 12 508 508 HOH HOH . 
W 4 HOH E 13 509 509 HOH HOH . 
W 4 HOH E 14 510 510 HOH HOH . 
W 4 HOH E 15 511 511 HOH HOH . 
W 4 HOH E 16 512 512 HOH HOH . 
W 4 HOH E 17 513 513 HOH HOH . 
W 4 HOH E 18 514 514 HOH HOH . 
W 4 HOH E 19 515 515 HOH HOH . 
W 4 HOH E 20 516 516 HOH HOH . 
W 4 HOH E 21 517 517 HOH HOH . 
W 4 HOH E 22 518 518 HOH HOH . 
W 4 HOH E 23 519 519 HOH HOH . 
W 4 HOH E 24 520 520 HOH HOH . 
W 4 HOH E 25 521 521 HOH HOH . 
W 4 HOH E 26 522 522 HOH HOH . 
W 4 HOH E 27 523 523 HOH HOH . 
W 4 HOH E 28 524 524 HOH HOH . 
X 4 HOH F 1 495 495 HOH HOH . 
X 4 HOH F 2 496 496 HOH HOH . 
X 4 HOH F 3 497 497 HOH HOH . 
X 4 HOH F 4 498 498 HOH HOH . 
X 4 HOH F 5 499 499 HOH HOH . 
X 4 HOH F 6 502 502 HOH HOH . 
X 4 HOH F 7 503 503 HOH HOH . 
X 4 HOH F 8 504 504 HOH HOH . 
X 4 HOH F 9 505 505 HOH HOH . 
X 4 HOH F 10 506 506 HOH HOH . 
X 4 HOH F 11 507 507 HOH HOH . 
X 4 HOH F 12 508 508 HOH HOH . 
X 4 HOH F 13 509 509 HOH HOH . 
X 4 HOH F 14 510 510 HOH HOH . 
X 4 HOH F 15 511 511 HOH HOH . 
X 4 HOH F 16 512 512 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' UDX . . . J 3 -10.72 45.119 59.486 1 44.61 ? C1' UDX 501 B 1 
HETATM 2 C C2' UDX . . . J 3 -11.565 43.963 60.054 1 46.11 ? C2' UDX 501 B 1 
HETATM 3 O O2' UDX . . . J 3 -12.679 43.724 59.195 1 46.54 ? O2' UDX 501 B 1 
HETATM 4 C C3' UDX . . . J 3 -12.049 44.298 61.477 1 47.06 ? C3' UDX 501 B 1 
HETATM 5 O O3' UDX . . . J 3 -12.53 43.132 62.196 1 46.59 ? O3' UDX 501 B 1 
HETATM 6 C C4' UDX . . . J 3 -10.882 44.962 62.228 1 46.54 ? C4' UDX 501 B 1 
HETATM 7 O O4' UDX . . . J 3 -11.184 45.078 63.615 1 48.58 ? O4' UDX 501 B 1 
HETATM 8 C C5' UDX . . . J 3 -10.592 46.328 61.615 1 44.59 ? C5' UDX 501 B 1 
HETATM 9 O O5' UDX . . . J 3 -9.902 45.887 60.455 1 44.38 ? O5' UDX 501 B 1 
HETATM 10 P PB UDX . . . J 3 -11.184 47.169 57.956 1 47.68 ? PB UDX 501 B 1 
HETATM 11 O O1B UDX . . . J 3 -9.723 47.387 57.741 1 47.98 ? O1B UDX 501 B 1 
HETATM 12 O O2B UDX . . . J 3 -11.834 48.522 58.502 1 48.24 ? O2B UDX 501 B 1 
HETATM 13 O O3B UDX . . . J 3 -11.65 45.956 58.879 1 44.14 ? O3B UDX 501 B 1 
HETATM 14 O O3A UDX . . . J 3 -12.038 46.984 56.606 1 48.82 ? O3A UDX 501 B 1 
HETATM 15 P PA UDX . . . J 3 -12.2 45.531 55.912 1 48.67 ? PA UDX 501 B 1 
HETATM 16 O O1A UDX . . . J 3 -13.55 45.272 55.321 1 46.87 ? O1A UDX 501 B 1 
HETATM 17 O O2A UDX . . . J 3 -11.667 44.371 56.939 1 46.38 ? O2A UDX 501 B 1 
HETATM 18 O O5D UDX . . . J 3 -11.097 45.57 54.775 1 46.48 ? O5D UDX 501 B 1 
HETATM 19 C C5D UDX . . . J 3 -9.695 45.502 55.038 1 43.61 ? C5D UDX 501 B 1 
HETATM 20 C C4D UDX . . . J 3 -8.937 45.453 53.714 1 40.68 ? C4D UDX 501 B 1 
HETATM 21 O O4D UDX . . . J 3 -9.29 44.157 53.231 1 40.86 ? O4D UDX 501 B 1 
HETATM 22 C C3D UDX . . . J 3 -9.555 46.473 52.76 1 38.45 ? C3D UDX 501 B 1 
HETATM 23 O O3D UDX . . . J 3 -8.515 47.194 52.135 1 35.94 ? O3D UDX 501 B 1 
HETATM 24 C C2D UDX . . . J 3 -10.397 45.648 51.776 1 38.43 ? C2D UDX 501 B 1 
HETATM 25 O O2D UDX . . . J 3 -10.343 46.186 50.465 1 37.84 ? O2D UDX 501 B 1 
HETATM 26 C C1D UDX . . . J 3 -9.704 44.301 51.84 1 40.21 ? C1D UDX 501 B 1 
HETATM 27 N N1 UDX . . . J 3 -10.588 43.16 51.458 1 41.08 ? N1 UDX 501 B 1 
HETATM 28 C C6 UDX . . . J 3 -11.642 42.73 52.246 1 41.88 ? C6 UDX 501 B 1 
HETATM 29 C C2 UDX . . . J 3 -10.315 42.488 50.304 1 41.35 ? C2 UDX 501 B 1 
HETATM 30 O O2 UDX . . . J 3 -9.362 42.859 49.633 1 43.93 ? O2 UDX 501 B 1 
HETATM 31 N N3 UDX . . . J 3 -11.09 41.422 49.897 1 41.94 ? N3 UDX 501 B 1 
HETATM 32 C C4 UDX . . . J 3 -12.162 40.982 50.665 1 42.9 ? C4 UDX 501 B 1 
HETATM 33 O O4 UDX . . . J 3 -12.856 40.015 50.308 1 42.88 ? O4 UDX 501 B 1 
HETATM 34 C C5 UDX . . . J 3 -12.423 41.652 51.851 1 42.95 ? C5 UDX 501 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           34 
#