data_3RUH
#
_model_server_result.job_id            ezS_aH0-FM43XtIeXbxSBQ 
_model_server_result.datetime_utc      '2025-07-12 19:12:10' 
_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          3ruh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":344}' 
#
_entry.id    3RUH 
#
_exptl.entry_id    3RUH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              606.366 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] hydrogen phosphate' 
_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            3RUH 
_cell.length_a            76.612 
_cell.length_b            76.612 
_cell.length_c            220.6 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RUH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
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,J,Q 1 1 
D,O,P,T 1 2 
B,C,K,L,M,N,R,S 2 1 
#
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' 2_554 -y,x-y,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 -73.533333 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
#
_chem_comp.formula           'C18 H28 N2 O17 P2' 
_chem_comp.formula_weight    606.366 
_chem_comp.id                UD6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] hydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     UDP-2-ketoGlc 
#
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
C2 N1 UD6 sing 437 n n 
N1 C6 UD6 sing 438 n n 
N1 C1B UD6 sing 439 n n 
N3 C2 UD6 sing 440 n n 
O2 C2 UD6 doub 441 n n 
N3 C4 UD6 sing 442 n n 
O4 C4 UD6 doub 443 n n 
C4 C5 UD6 sing 444 n n 
C5 C6 UD6 doub 445 n n 
C5 H5 UD6 sing 446 n n 
C6 H6 UD6 sing 447 n n 
O2A PA UD6 doub 448 n n 
O5B PA UD6 sing 449 n n 
PA O1A UD6 sing 450 n n 
PA O3A UD6 sing 451 n n 
O3A PB UD6 sing 452 n n 
O1B PB UD6 doub 453 n n 
PB O1' UD6 sing 454 n n 
PB O2B UD6 sing 455 n n 
O1' C1' UD6 sing 456 n n 
C1' O5' UD6 sing 457 n n 
C1' C2' UD6 sing 458 n n 
C1' H1' UD6 sing 459 n n 
O1A HO1A UD6 sing 460 n n 
O4B C1B UD6 sing 461 n n 
C1B C2B UD6 sing 462 n n 
C1B H1B UD6 sing 463 n n 
C3' C2' UD6 sing 464 n n 
C9' C2' UD6 sing 465 n n 
C2' H2' UD6 sing 466 n n 
C2B O2' UD6 sing 467 n n 
O2' HO2' UD6 sing 468 n n 
C2B C3B UD6 sing 469 n n 
C2B H2B UD6 sing 470 n n 
O2B HO2B UD6 sing 471 n n 
C3' C4' UD6 sing 472 n n 
C3' O3' UD6 sing 473 n n 
C3' H3' UD6 sing 474 n n 
O3' HO3' UD6 sing 475 n n 
C4B C3B UD6 sing 476 n n 
O3B C3B UD6 sing 477 n n 
C3B H3B UD6 sing 478 n n 
O3B HO3B UD6 sing 479 n n 
C5' C4' UD6 sing 480 n n 
C4' O4' UD6 sing 481 n n 
C4' H4' UD6 sing 482 n n 
O4' HO4' UD6 sing 483 n n 
O4B C4B UD6 sing 484 n n 
C4B C5B UD6 sing 485 n n 
C4B H4B UD6 sing 486 n n 
C5' C6' UD6 sing 487 n n 
C5' O5' UD6 sing 488 n n 
C5' H5' UD6 sing 489 n n 
C5B O5B UD6 sing 490 n n 
C5B H5B UD6 sing 491 n n 
C5B H5BA UD6 sing 492 n n 
C6' O6' UD6 sing 493 n n 
C6' H6' UD6 sing 494 n n 
C6' "H6'A" UD6 sing 495 n n 
O6' HO6' UD6 sing 496 n n 
C8' C7' UD6 sing 497 n n 
C9' C7' UD6 sing 498 n n 
C7' O7' UD6 doub 499 n n 
C8' H8' UD6 sing 500 n n 
C8' "H8'A" UD6 sing 501 n n 
C8' "H8'B" UD6 sing 502 n n 
C9' H9' UD6 sing 503 n n 
C9' "H9'A" UD6 sing 504 n n 
N3 HN3 UD6 sing 505 n n 
#
_atom_sites.entry_id                     3RUH 
_atom_sites.fract_transf_matrix[1][1]    0.013053 
_atom_sites.fract_transf_matrix[1][2]    0.007536 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015072 
_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]    0.004533 
_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 NAD A 1 343 343 NAD NAD . 
F 3 UD6 A 1 344 344 UD6 UD6 . 
G 4 SO4 A 1 345 1 SO4 SO4 . 
H 4 SO4 A 1 346 2 SO4 SO4 . 
I 4 SO4 A 1 347 3 SO4 SO4 . 
J 5 NA A 1 348 1 NA NA . 
K 2 NAD B 1 343 343 NAD NAD . 
L 3 UD6 B 1 344 344 UD6 UD6 . 
M 2 NAD C 1 343 343 NAD NAD . 
N 3 UD6 C 1 344 344 UD6 UD6 . 
O 2 NAD D 1 343 343 NAD NAD . 
P 3 UD6 D 1 344 344 UD6 UD6 . 
Q 6 HOH A 1 349 15 HOH HOH . 
Q 6 HOH A 2 350 19 HOH HOH . 
Q 6 HOH A 3 351 23 HOH HOH . 
Q 6 HOH A 4 352 31 HOH HOH . 
Q 6 HOH A 5 353 32 HOH HOH . 
Q 6 HOH A 6 354 38 HOH HOH . 
Q 6 HOH A 7 355 41 HOH HOH . 
R 6 HOH B 1 345 4 HOH HOH . 
R 6 HOH B 2 346 6 HOH HOH . 
R 6 HOH B 3 347 9 HOH HOH . 
R 6 HOH B 4 348 17 HOH HOH . 
R 6 HOH B 5 349 21 HOH HOH . 
R 6 HOH B 6 350 24 HOH HOH . 
R 6 HOH B 7 351 27 HOH HOH . 
R 6 HOH B 8 352 29 HOH HOH . 
R 6 HOH B 9 353 34 HOH HOH . 
R 6 HOH B 10 354 37 HOH HOH . 
S 6 HOH C 1 345 1 HOH HOH . 
S 6 HOH C 2 346 2 HOH HOH . 
S 6 HOH C 3 347 5 HOH HOH . 
S 6 HOH C 4 348 10 HOH HOH . 
S 6 HOH C 5 349 11 HOH HOH . 
S 6 HOH C 6 350 12 HOH HOH . 
S 6 HOH C 7 351 14 HOH HOH . 
S 6 HOH C 8 352 16 HOH HOH . 
S 6 HOH C 9 353 20 HOH HOH . 
S 6 HOH C 10 354 22 HOH HOH . 
S 6 HOH C 11 355 25 HOH HOH . 
S 6 HOH C 12 356 36 HOH HOH . 
S 6 HOH C 13 357 39 HOH HOH . 
T 6 HOH D 1 345 3 HOH HOH . 
T 6 HOH D 2 346 7 HOH HOH . 
T 6 HOH D 3 347 8 HOH HOH . 
T 6 HOH D 4 348 13 HOH HOH . 
T 6 HOH D 5 349 18 HOH HOH . 
T 6 HOH D 6 350 26 HOH HOH . 
T 6 HOH D 7 351 28 HOH HOH . 
T 6 HOH D 8 352 30 HOH HOH . 
T 6 HOH D 9 353 33 HOH HOH . 
T 6 HOH D 10 354 35 HOH HOH . 
T 6 HOH D 11 355 40 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 N N1 UD6 . . . N 3 13.514 -50.76 58.219 1 40.82 ? N1 UD6 344 C 1 
HETATM 2 C C2 UD6 . . . N 3 12.655 -51.011 59.3 1 42.64 ? C2 UD6 344 C 1 
HETATM 3 O O2 UD6 . . . N 3 12.582 -52.141 59.793 1 44.3 ? O2 UD6 344 C 1 
HETATM 4 N N3 UD6 . . . N 3 11.878 -49.959 59.806 1 42.49 ? N3 UD6 344 C 1 
HETATM 5 C C4 UD6 . . . N 3 11.956 -48.681 59.245 1 40.73 ? C4 UD6 344 C 1 
HETATM 6 O O4 UD6 . . . N 3 11.27 -47.769 59.702 1 41.54 ? O4 UD6 344 C 1 
HETATM 7 C C5 UD6 . . . N 3 12.81 -48.433 58.177 1 38.95 ? C5 UD6 344 C 1 
HETATM 8 C C6 UD6 . . . N 3 13.591 -49.461 57.665 1 38.7 ? C6 UD6 344 C 1 
HETATM 9 P PA UD6 . . . N 3 17.375 -48.798 55.19 1 32.81 ? PA UD6 344 C 1 
HETATM 10 P PB UD6 . . . N 3 18.341 -50.236 52.847 1 32.76 ? PB UD6 344 C 1 
HETATM 11 C C1' UD6 . . . N 3 19.596 -49.495 50.653 0.7 30.9 ? C1' UD6 344 C 1 
HETATM 12 O O1' UD6 . . . N 3 19.494 -49.432 52.069 1 30.61 ? O1' UD6 344 C 1 
HETATM 13 O O1A UD6 . . . N 3 16.212 -47.891 55.183 1 33.51 ? O1A UD6 344 C 1 
HETATM 14 C C1B UD6 . . . N 3 14.342 -51.868 57.676 1 40.36 ? C1B UD6 344 C 1 
HETATM 15 O O1B UD6 . . . N 3 18.982 -51.25 53.709 1 32.58 ? O1B UD6 344 C 1 
HETATM 16 C C2' UD6 . . . N 3 20.986 -50.068 50.304 0.7 30.68 ? C2' UD6 344 C 1 
HETATM 17 O O2' UD6 . . . N 3 13.104 -52.904 55.887 1 41.6 ? O2' UD6 344 C 1 
HETATM 18 O O2A UD6 . . . N 3 18.543 -48.457 56.033 1 32.42 ? O2A UD6 344 C 1 
HETATM 19 C C2B UD6 . . . N 3 14.169 -51.994 56.163 1 39.55 ? C2B UD6 344 C 1 
HETATM 20 O O2B UD6 . . . N 3 17.272 -50.66 51.909 1 33.1 ? O2B UD6 344 C 1 
HETATM 21 C C3' UD6 . . . N 3 22.067 -49.108 50.803 0.7 29.9 ? C3' UD6 344 C 1 
HETATM 22 O O3' UD6 . . . N 3 23.363 -49.532 50.378 0.7 28.99 ? O3' UD6 344 C 1 
HETATM 23 O O3A UD6 . . . N 3 17.837 -48.92 53.661 1 32.45 ? O3A UD6 344 C 1 
HETATM 24 C C3B UD6 . . . N 3 15.499 -52.593 55.728 1 37.97 ? C3B UD6 344 C 1 
HETATM 25 O O3B UD6 . . . N 3 15.385 -54.021 55.667 1 39.02 ? O3B UD6 344 C 1 
HETATM 26 C C4' UD6 . . . N 3 21.778 -47.693 50.271 0.7 29.23 ? C4' UD6 344 C 1 
HETATM 27 O O4' UD6 . . . N 3 21.972 -47.66 48.852 0.7 28.07 ? O4' UD6 344 C 1 
HETATM 28 C C4B UD6 . . . N 3 16.482 -52.191 56.848 1 37.36 ? C4B UD6 344 C 1 
HETATM 29 O O4B UD6 . . . N 3 15.719 -51.524 57.87 1 38.76 ? O4B UD6 344 C 1 
HETATM 30 C C5' UD6 . . . N 3 20.362 -47.22 50.646 0.7 29.91 ? C5' UD6 344 C 1 
HETATM 31 O O5' UD6 . . . N 3 19.385 -48.159 50.137 0.7 30.03 ? O5' UD6 344 C 1 
HETATM 32 C C5B UD6 . . . N 3 17.469 -51.127 56.417 1 34.23 ? C5B UD6 344 C 1 
HETATM 33 O O5B UD6 . . . N 3 16.827 -50.26 55.515 1 33.72 ? O5B UD6 344 C 1 
HETATM 34 C C6' UD6 . . . N 3 20.052 -45.812 50.13 0.7 29.5 ? C6' UD6 344 C 1 
HETATM 35 O O6' UD6 . . . N 3 18.855 -45.358 50.769 0.7 30.95 ? O6' UD6 344 C 1 
HETATM 36 C C7' UD6 . . . N 3 20.585 -52.583 50.346 0.7 33.11 ? C7' UD6 344 C 1 
HETATM 37 O O7' UD6 . . . N 3 19.89 -52.468 49.334 0.7 33.44 ? O7' UD6 344 C 1 
HETATM 38 C C8' UD6 . . . N 3 20.8 -53.954 50.994 0.7 34.38 ? C8' UD6 344 C 1 
HETATM 39 C C9' UD6 . . . N 3 21.179 -51.462 50.92 0.7 31.88 ? C9' UD6 344 C 1 
#
_model_server_stats.io_time_ms              36 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           39 
#