data_8WOV
#
_model_server_result.job_id            GLhalRZBjnV9wIerloaWFg 
_model_server_result.datetime_utc      '2024-11-22 18:35:35' 
_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          8wov 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    8WOV 
#
_exptl.entry_id    8WOV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            8WOV 
_cell.length_a            101.49 
_cell.length_b            109.243 
_cell.length_c            130.627 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WOV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 D N N 
? 3 E 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 433 n n 
N1 C6 UDP sing 434 n n 
N1 C1' UDP sing 435 n n 
C2 N3 UDP sing 436 n n 
C2 O2 UDP doub 437 n n 
N3 C4 UDP sing 438 n n 
N3 HN3 UDP sing 439 n n 
C4 C5 UDP sing 440 n n 
C4 O4 UDP doub 441 n n 
C5 C6 UDP doub 442 n n 
C5 H5 UDP sing 443 n n 
C6 H6 UDP sing 444 n n 
C1' C2' UDP sing 445 n n 
C1' O4' UDP sing 446 n n 
C1' H1' UDP sing 447 n n 
C2' O2' UDP sing 448 n n 
C2' C3' UDP sing 449 n n 
C2' H2' UDP sing 450 n n 
O2' HO2' UDP sing 451 n n 
C3' C4' UDP sing 452 n n 
C3' O3' UDP sing 453 n n 
C3' H3' UDP sing 454 n n 
C4' O4' UDP sing 455 n n 
C4' C5' UDP sing 456 n n 
C4' H4' UDP sing 457 n n 
O3' HO3' UDP sing 458 n n 
C5' O5' UDP sing 459 n n 
C5' "H5'1" UDP sing 460 n n 
C5' "H5'2" UDP sing 461 n n 
O5' PA UDP sing 462 n n 
PA O1A UDP doub 463 n n 
PA O2A UDP sing 464 n n 
PA O3A UDP sing 465 n n 
O2A HOA2 UDP sing 466 n n 
O3A PB UDP sing 467 n n 
PB O1B UDP doub 468 n n 
PB O2B UDP sing 469 n n 
PB O3B UDP sing 470 n n 
O2B HOB2 UDP sing 471 n n 
O3B HOB3 UDP sing 472 n n 
#
_atom_sites.entry_id                     8WOV 
_atom_sites.fract_transf_matrix[1][1]    0.009853 
_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]    0.009154 
_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]    0.007655 
_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
C 2 NAD B 1 401 401 NAD NAD . 
D 3 UDP B 1 402 402 UDP UDP . 
E 3 UDP A 1 401 401 UDP UDP . 
F 2 NAD A 1 402 402 NAD NAD . 
G 4 HOH B 1 501 66 HOH HOH . 
G 4 HOH B 2 502 53 HOH HOH . 
G 4 HOH B 3 503 18 HOH HOH . 
G 4 HOH B 4 504 95 HOH HOH . 
G 4 HOH B 5 505 59 HOH HOH . 
G 4 HOH B 6 506 11 HOH HOH . 
G 4 HOH B 7 507 34 HOH HOH . 
G 4 HOH B 8 508 42 HOH HOH . 
G 4 HOH B 9 509 81 HOH HOH . 
G 4 HOH B 10 510 102 HOH HOH . 
G 4 HOH B 11 511 64 HOH HOH . 
G 4 HOH B 12 512 8 HOH HOH . 
G 4 HOH B 13 513 91 HOH HOH . 
G 4 HOH B 14 514 65 HOH HOH . 
G 4 HOH B 15 515 84 HOH HOH . 
G 4 HOH B 16 516 27 HOH HOH . 
G 4 HOH B 17 517 12 HOH HOH . 
G 4 HOH B 18 518 51 HOH HOH . 
G 4 HOH B 19 519 80 HOH HOH . 
G 4 HOH B 20 520 15 HOH HOH . 
G 4 HOH B 21 521 69 HOH HOH . 
G 4 HOH B 22 522 75 HOH HOH . 
G 4 HOH B 23 523 90 HOH HOH . 
G 4 HOH B 24 524 56 HOH HOH . 
G 4 HOH B 25 525 77 HOH HOH . 
G 4 HOH B 26 526 57 HOH HOH . 
G 4 HOH B 27 527 79 HOH HOH . 
G 4 HOH B 28 528 33 HOH HOH . 
G 4 HOH B 29 529 97 HOH HOH . 
G 4 HOH B 30 530 20 HOH HOH . 
G 4 HOH B 31 531 13 HOH HOH . 
G 4 HOH B 32 532 37 HOH HOH . 
G 4 HOH B 33 533 21 HOH HOH . 
G 4 HOH B 34 534 23 HOH HOH . 
G 4 HOH B 35 535 29 HOH HOH . 
G 4 HOH B 36 536 48 HOH HOH . 
G 4 HOH B 37 537 9 HOH HOH . 
G 4 HOH B 38 538 104 HOH HOH . 
G 4 HOH B 39 539 105 HOH HOH . 
G 4 HOH B 40 540 107 HOH HOH . 
G 4 HOH B 41 541 30 HOH HOH . 
G 4 HOH B 42 542 47 HOH HOH . 
G 4 HOH B 43 543 85 HOH HOH . 
G 4 HOH B 44 544 70 HOH HOH . 
G 4 HOH B 45 545 44 HOH HOH . 
G 4 HOH B 46 546 4 HOH HOH . 
G 4 HOH B 47 547 46 HOH HOH . 
G 4 HOH B 48 548 88 HOH HOH . 
H 4 HOH A 1 501 2 HOH HOH . 
H 4 HOH A 2 502 62 HOH HOH . 
H 4 HOH A 3 503 38 HOH HOH . 
H 4 HOH A 4 504 98 HOH HOH . 
H 4 HOH A 5 505 49 HOH HOH . 
H 4 HOH A 6 506 31 HOH HOH . 
H 4 HOH A 7 507 39 HOH HOH . 
H 4 HOH A 8 508 72 HOH HOH . 
H 4 HOH A 9 509 43 HOH HOH . 
H 4 HOH A 10 510 61 HOH HOH . 
H 4 HOH A 11 511 55 HOH HOH . 
H 4 HOH A 12 512 14 HOH HOH . 
H 4 HOH A 13 513 100 HOH HOH . 
H 4 HOH A 14 514 58 HOH HOH . 
H 4 HOH A 15 515 78 HOH HOH . 
H 4 HOH A 16 516 32 HOH HOH . 
H 4 HOH A 17 517 25 HOH HOH . 
H 4 HOH A 18 518 35 HOH HOH . 
H 4 HOH A 19 519 103 HOH HOH . 
H 4 HOH A 20 520 52 HOH HOH . 
H 4 HOH A 21 521 74 HOH HOH . 
H 4 HOH A 22 522 89 HOH HOH . 
H 4 HOH A 23 523 50 HOH HOH . 
H 4 HOH A 24 524 5 HOH HOH . 
H 4 HOH A 25 525 82 HOH HOH . 
H 4 HOH A 26 526 71 HOH HOH . 
H 4 HOH A 27 527 6 HOH HOH . 
H 4 HOH A 28 528 22 HOH HOH . 
H 4 HOH A 29 529 67 HOH HOH . 
H 4 HOH A 30 530 93 HOH HOH . 
H 4 HOH A 31 531 16 HOH HOH . 
H 4 HOH A 32 532 24 HOH HOH . 
H 4 HOH A 33 533 40 HOH HOH . 
H 4 HOH A 34 534 10 HOH HOH . 
H 4 HOH A 35 535 63 HOH HOH . 
H 4 HOH A 36 536 28 HOH HOH . 
H 4 HOH A 37 537 108 HOH HOH . 
H 4 HOH A 38 538 41 HOH HOH . 
H 4 HOH A 39 539 99 HOH HOH . 
H 4 HOH A 40 540 109 HOH HOH . 
H 4 HOH A 41 541 76 HOH HOH . 
H 4 HOH A 42 542 86 HOH HOH . 
H 4 HOH A 43 543 60 HOH HOH . 
H 4 HOH A 44 544 87 HOH HOH . 
H 4 HOH A 45 545 101 HOH HOH . 
H 4 HOH A 46 546 3 HOH HOH . 
H 4 HOH A 47 547 19 HOH HOH . 
H 4 HOH A 48 548 1 HOH HOH . 
H 4 HOH A 49 549 83 HOH HOH . 
H 4 HOH A 50 550 17 HOH HOH . 
H 4 HOH A 51 551 45 HOH HOH . 
H 4 HOH A 52 552 7 HOH HOH . 
H 4 HOH A 53 553 54 HOH HOH . 
H 4 HOH A 54 554 96 HOH HOH . 
H 4 HOH A 55 555 73 HOH HOH . 
H 4 HOH A 56 556 92 HOH HOH . 
H 4 HOH A 57 557 36 HOH HOH . 
H 4 HOH A 58 558 26 HOH HOH . 
H 4 HOH A 59 559 106 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 . . . E 3 49.275 23.815 13.444 1 31.21 ? N1 UDP 401 A 1 
HETATM 2 C C2 UDP . . . E 3 50.348 24.455 14.044 1 30.24 ? C2 UDP 401 A 1 
HETATM 3 N N3 UDP . . . E 3 50.029 25.63 14.675 1 29.3 ? N3 UDP 401 A 1 
HETATM 4 C C4 UDP . . . E 3 48.777 26.217 14.785 1 30.4 ? C4 UDP 401 A 1 
HETATM 5 C C5 UDP . . . E 3 47.717 25.492 14.138 1 26.47 ? C5 UDP 401 A 1 
HETATM 6 C C6 UDP . . . E 3 47.996 24.335 13.514 1 30.9 ? C6 UDP 401 A 1 
HETATM 7 O O2 UDP . . . E 3 51.496 24.019 14.024 1 31.96 ? O2 UDP 401 A 1 
HETATM 8 O O4 UDP . . . E 3 48.661 27.27 15.425 1 29.79 ? O4 UDP 401 A 1 
HETATM 9 C C1' UDP . . . E 3 49.558 22.563 12.71 1 31.81 ? C1' UDP 401 A 1 
HETATM 10 C C2' UDP . . . E 3 48.754 21.379 13.226 1 32.58 ? C2' UDP 401 A 1 
HETATM 11 O O2' UDP . . . E 3 49.563 20.854 14.253 1 36.35 ? O2' UDP 401 A 1 
HETATM 12 C C3' UDP . . . E 3 48.672 20.527 11.961 1 29.58 ? C3' UDP 401 A 1 
HETATM 13 C C4' UDP . . . E 3 48.517 21.575 10.85 1 28.14 ? C4' UDP 401 A 1 
HETATM 14 O O4' UDP . . . E 3 49.204 22.737 11.356 1 30.1 ? O4' UDP 401 A 1 
HETATM 15 O O3' UDP . . . E 3 49.883 19.801 11.835 1 33.45 ? O3' UDP 401 A 1 
HETATM 16 C C5' UDP . . . E 3 47.113 21.967 10.491 1 28.04 ? C5' UDP 401 A 1 
HETATM 17 O O5' UDP . . . E 3 46.337 21.961 11.722 1 30.87 ? O5' UDP 401 A 1 
HETATM 18 P PA UDP . . . E 3 44.837 22.495 11.754 1 29.15 ? PA UDP 401 A 1 
HETATM 19 O O1A UDP . . . E 3 44.684 23.557 10.722 1 26.25 ? O1A UDP 401 A 1 
HETATM 20 O O2A UDP . . . E 3 44.463 22.781 13.19 1 35.88 ? O2A UDP 401 A 1 
HETATM 21 O O3A UDP . . . E 3 43.981 21.274 11.295 1 29.34 ? O3A UDP 401 A 1 
HETATM 22 P PB UDP . . . E 3 43.784 19.732 11.64 1 43.04 ? PB UDP 401 A 1 
HETATM 23 O O1B UDP . . . E 3 44.908 19.147 10.832 1 34.85 ? O1B UDP 401 A 1 
HETATM 24 O O2B UDP . . . E 3 43.936 19.545 13.161 1 34.18 ? O2B UDP 401 A 1 
HETATM 25 O O3B UDP . . . E 3 42.331 19.406 11.085 1 37.77 ? O3B UDP 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           25 
#