data_3RUH
#
_model_server_result.job_id            CrE71bQJDnSygg_4nBsjIg 
_model_server_result.datetime_utc      '2025-02-20 15:30:27' 
_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":"P","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 . . . P 3 -24.903 -15.693 43.212 1 42.45 ? N1 UD6 344 D 1 
HETATM 2 C C2 UD6 . . . P 3 -25.765 -15.437 42.132 1 44.54 ? C2 UD6 344 D 1 
HETATM 3 O O2 UD6 . . . P 3 -25.89 -14.296 41.679 1 46.19 ? O2 UD6 344 D 1 
HETATM 4 N N3 UD6 . . . P 3 -26.493 -16.502 41.578 1 44.61 ? N3 UD6 344 D 1 
HETATM 5 C C4 UD6 . . . P 3 -26.356 -17.798 42.089 1 42.69 ? C4 UD6 344 D 1 
HETATM 6 O O4 UD6 . . . P 3 -26.996 -18.717 41.591 1 43.48 ? O4 UD6 344 D 1 
HETATM 7 C C5 UD6 . . . P 3 -25.502 -18.053 43.156 1 40.9 ? C5 UD6 344 D 1 
HETATM 8 C C6 UD6 . . . P 3 -24.772 -17.01 43.713 1 40.62 ? C6 UD6 344 D 1 
HETATM 9 P PA UD6 . . . P 3 -20.729 -17.521 46.043 1 34.58 ? PA UD6 344 D 1 
HETATM 10 P PB UD6 . . . P 3 -19.999 -16.123 48.513 1 34.66 ? PB UD6 344 D 1 
HETATM 11 C C1' UD6 . . . P 3 -18.685 -16.582 50.664 0.7 32.59 ? C1' UD6 344 D 1 
HETATM 12 O O1' UD6 . . . P 3 -18.676 -16.535 49.256 1 32.62 ? O1' UD6 344 D 1 
HETATM 13 O O1A UD6 . . . P 3 -21.801 -18.536 46.092 1 35.43 ? O1A UD6 344 D 1 
HETATM 14 C C1B UD6 . . . P 3 -24.125 -14.577 43.808 1 42.28 ? C1B UD6 344 D 1 
HETATM 15 O O1B UD6 . . . P 3 -19.713 -14.836 47.836 1 34.54 ? O1B UD6 344 D 1 
HETATM 16 C C2' UD6 . . . P 3 -17.274 -16.235 51.153 0.7 31.69 ? C2' UD6 344 D 1 
HETATM 17 O O2' UD6 . . . P 3 -25.404 -13.658 45.624 1 42.92 ? O2' UD6 344 D 1 
HETATM 18 O O2A UD6 . . . P 3 -19.634 -17.674 45.061 1 34.13 ? O2A UD6 344 D 1 
HETATM 19 C C2B UD6 . . . P 3 -24.276 -14.477 45.324 1 41.32 ? C2B UD6 344 D 1 
HETATM 20 O O2B UD6 . . . P 3 -21.152 -16.225 49.439 1 35.69 ? O2B UD6 344 D 1 
HETATM 21 C C3' UD6 . . . P 3 -16.316 -17.283 50.607 0.7 30.63 ? C3' UD6 344 D 1 
HETATM 22 O O3' UD6 . . . P 3 -15.035 -17.098 51.197 0.7 29.55 ? O3' UD6 344 D 1 
HETATM 23 O O3A UD6 . . . P 3 -20.066 -17.419 47.518 1 34.11 ? O3A UD6 344 D 1 
HETATM 24 C C3B UD6 . . . P 3 -22.982 -13.774 45.723 1 39.93 ? C3B UD6 344 D 1 
HETATM 25 O O3B UD6 . . . P 3 -23.176 -12.352 45.72 1 41.4 ? O3B UD6 344 D 1 
HETATM 26 C C4' UD6 . . . P 3 -16.838 -18.705 50.902 0.7 30.61 ? C4' UD6 344 D 1 
HETATM 27 O O4' UD6 . . . P 3 -16.754 -18.968 52.31 0.7 29.2 ? O4' UD6 344 D 1 
HETATM 28 C C4B UD6 . . . P 3 -21.999 -14.142 44.597 1 39.63 ? C4B UD6 344 D 1 
HETATM 29 O O4B UD6 . . . P 3 -22.74 -14.888 43.617 1 41.12 ? O4B UD6 344 D 1 
HETATM 30 C C5' UD6 . . . P 3 -18.279 -18.927 50.372 0.7 31.52 ? C5' UD6 344 D 1 
HETATM 31 O O5' UD6 . . . P 3 -19.119 -17.925 50.989 0.7 32.23 ? O5' UD6 344 D 1 
HETATM 32 C C5B UD6 . . . P 3 -20.906 -15.1 45.03 1 36.8 ? C5B UD6 344 D 1 
HETATM 33 O O5B UD6 . . . P 3 -21.452 -16.104 45.861 1 35.71 ? O5B UD6 344 D 1 
HETATM 34 C C6' UD6 . . . P 3 -18.95 -20.304 50.6 0.7 31.13 ? C6' UD6 344 D 1 
HETATM 35 O O6' UD6 . . . P 3 -18.149 -21.145 51.439 0.7 29.43 ? O6' UD6 344 D 1 
HETATM 36 C C7' UD6 . . . P 3 -17.465 -13.655 51.09 0.7 34.18 ? C7' UD6 344 D 1 
HETATM 37 O O7' UD6 . . . P 3 -18.442 -13.687 51.84 0.7 35.18 ? O7' UD6 344 D 1 
HETATM 38 C C8' UD6 . . . P 3 -16.942 -12.315 50.578 0.7 35.17 ? C8' UD6 344 D 1 
HETATM 39 C C9' UD6 . . . P 3 -16.832 -14.832 50.684 0.7 32.88 ? C9' UD6 344 D 1 
#
_model_server_stats.io_time_ms              88 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           39 
#