data_8OOJ
#
_model_server_result.job_id            '_LuC_kH9ofyjJkZ9tjekgA' 
_model_server_result.datetime_utc      '2024-10-13 09:13:00' 
_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          8ooj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":301}' 
#
_entry.id    8OOJ 
#
_exptl.entry_id    8OOJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            8OOJ 
_cell.length_a            137.47 
_cell.length_b            138.389 
_cell.length_c            116.825 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8OOJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,M,N 1 1 
C,I,J,O 2 1,2 
D,K,L,P 3 1,3 
#
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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 58.4125 
3 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.4125 
#
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 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
N1 C2 UDP sing 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     8OOJ 
_atom_sites.fract_transf_matrix[1][1]    0.007274 
_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]    0.007226 
_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]    0.00856 
_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 UDP A 1 301 301 UDP UDP . 
F 3 VVC A 1 302 302 VVC DRG . 
G 2 UDP B 1 301 301 UDP UDP . 
H 3 VVC B 1 302 302 VVC DRG . 
I 2 UDP C 1 301 301 UDP UDP . 
J 3 VVC C 1 302 302 VVC DRG . 
K 2 UDP D 1 301 301 UDP UDP . 
L 3 VVC D 1 302 302 VVC DRG . 
M 4 HOH A 1 401 41 HOH HOH . 
M 4 HOH A 2 402 48 HOH HOH . 
M 4 HOH A 3 403 24 HOH HOH . 
M 4 HOH A 4 404 10 HOH HOH . 
M 4 HOH A 5 405 42 HOH HOH . 
M 4 HOH A 6 406 38 HOH HOH . 
N 4 HOH B 1 401 43 HOH HOH . 
N 4 HOH B 2 402 52 HOH HOH . 
N 4 HOH B 3 403 49 HOH HOH . 
N 4 HOH B 4 404 3 HOH HOH . 
N 4 HOH B 5 405 9 HOH HOH . 
N 4 HOH B 6 406 17 HOH HOH . 
N 4 HOH B 7 407 18 HOH HOH . 
N 4 HOH B 8 408 39 HOH HOH . 
N 4 HOH B 9 409 37 HOH HOH . 
N 4 HOH B 10 410 2 HOH HOH . 
N 4 HOH B 11 411 20 HOH HOH . 
N 4 HOH B 12 412 5 HOH HOH . 
N 4 HOH B 13 413 50 HOH HOH . 
N 4 HOH B 14 414 53 HOH HOH . 
N 4 HOH B 15 415 12 HOH HOH . 
N 4 HOH B 16 416 47 HOH HOH . 
N 4 HOH B 17 417 29 HOH HOH . 
N 4 HOH B 18 418 22 HOH HOH . 
N 4 HOH B 19 419 26 HOH HOH . 
O 4 HOH C 1 401 23 HOH HOH . 
O 4 HOH C 2 402 33 HOH HOH . 
O 4 HOH C 3 403 35 HOH HOH . 
O 4 HOH C 4 404 25 HOH HOH . 
O 4 HOH C 5 405 30 HOH HOH . 
O 4 HOH C 6 406 46 HOH HOH . 
O 4 HOH C 7 407 51 HOH HOH . 
O 4 HOH C 8 408 8 HOH HOH . 
O 4 HOH C 9 409 21 HOH HOH . 
O 4 HOH C 10 410 40 HOH HOH . 
O 4 HOH C 11 411 1 HOH HOH . 
O 4 HOH C 12 412 13 HOH HOH . 
O 4 HOH C 13 413 16 HOH HOH . 
O 4 HOH C 14 414 34 HOH HOH . 
O 4 HOH C 15 415 36 HOH HOH . 
P 4 HOH D 1 401 44 HOH HOH . 
P 4 HOH D 2 402 27 HOH HOH . 
P 4 HOH D 3 403 28 HOH HOH . 
P 4 HOH D 4 404 14 HOH HOH . 
P 4 HOH D 5 405 6 HOH HOH . 
P 4 HOH D 6 406 7 HOH HOH . 
P 4 HOH D 7 407 19 HOH HOH . 
P 4 HOH D 8 408 32 HOH HOH . 
P 4 HOH D 9 409 45 HOH HOH . 
P 4 HOH D 10 410 11 HOH HOH . 
P 4 HOH D 11 411 4 HOH HOH . 
P 4 HOH D 12 412 15 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 UDP . . . I 2 29.637 -60.818 14.511 1 49.96 ? N1 UDP 301 C 1 
HETATM 2 C C2 UDP . . . I 2 30.814 -61.037 13.81 1 52.34 ? C2 UDP 301 C 1 
HETATM 3 N N3 UDP . . . I 2 31.041 -60.157 12.782 1 53.98 ? N3 UDP 301 C 1 
HETATM 4 C C4 UDP . . . I 2 30.236 -59.106 12.385 1 53.73 ? C4 UDP 301 C 1 
HETATM 5 C C5 UDP . . . I 2 29.039 -58.946 13.157 1 52.9 ? C5 UDP 301 C 1 
HETATM 6 C C6 UDP . . . I 2 28.789 -59.789 14.171 1 53.15 ? C6 UDP 301 C 1 
HETATM 7 O O2 UDP . . . I 2 31.606 -61.935 14.074 1 53.26 ? O2 UDP 301 C 1 
HETATM 8 O O4 UDP . . . I 2 30.582 -58.404 11.435 1 56.98 ? O4 UDP 301 C 1 
HETATM 9 C C1' UDP . . . I 2 29.316 -61.717 15.639 1 45.93 ? C1' UDP 301 C 1 
HETATM 10 C C2' UDP . . . I 2 29.2 -60.98 16.972 1 45.05 ? C2' UDP 301 C 1 
HETATM 11 O O2' UDP . . . I 2 30.471 -60.81 17.562 1 43.53 ? O2' UDP 301 C 1 
HETATM 12 C C3' UDP . . . I 2 28.292 -61.936 17.757 1 44.1 ? C3' UDP 301 C 1 
HETATM 13 C C4' UDP . . . I 2 27.371 -62.515 16.671 1 44.33 ? C4' UDP 301 C 1 
HETATM 14 O O4' UDP . . . I 2 28.051 -62.293 15.405 1 44.08 ? O4' UDP 301 C 1 
HETATM 15 O O3' UDP . . . I 2 29.011 -62.972 18.41 1 44.43 ? O3' UDP 301 C 1 
HETATM 16 C C5' UDP . . . I 2 25.979 -61.936 16.613 1 45.33 ? C5' UDP 301 C 1 
HETATM 17 O O5' UDP . . . I 2 26.043 -60.497 16.413 1 43.39 ? O5' UDP 301 C 1 
HETATM 18 P PA UDP . . . I 2 25.141 -59.552 17.342 1 39.78 ? PA UDP 301 C 1 
HETATM 19 O O1A UDP . . . I 2 25.489 -58.126 17.076 1 41.12 ? O1A UDP 301 C 1 
HETATM 20 O O2A UDP . . . I 2 25.19 -60.047 18.751 1 35.16 ? O2A UDP 301 C 1 
HETATM 21 O O3A UDP . . . I 2 23.705 -59.846 16.707 1 41.15 ? O3A UDP 301 C 1 
HETATM 22 P PB UDP . . . I 2 22.201 -59.302 16.951 1 40.99 ? PB UDP 301 C 1 
HETATM 23 O O1B UDP . . . I 2 21.681 -58.846 15.607 1 40.54 ? O1B UDP 301 C 1 
HETATM 24 O O2B UDP . . . I 2 21.474 -60.505 17.465 1 38.99 ? O2B UDP 301 C 1 
HETATM 25 O O3B UDP . . . I 2 22.318 -58.197 17.966 1 36.87 ? O3B UDP 301 C 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#