data_8B63
#
_model_server_result.job_id            bIgVQmMO4QB1_E52wx9cVQ 
_model_server_result.datetime_utc      '2024-11-13 22:34:31' 
_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          8b63 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    8B63 
#
_exptl.entry_id    8B63 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.22 
_cell.angle_gamma         90 
_cell.entry_id            8B63 
_cell.length_a            41.762 
_cell.length_b            109.963 
_cell.length_c            94.326 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8B63 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 432 n n 
N1 C6 UDP sing 433 n n 
N1 C1' UDP sing 434 n n 
C2 N3 UDP sing 435 n n 
C2 O2 UDP doub 436 n n 
N3 C4 UDP sing 437 n n 
N3 HN3 UDP sing 438 n n 
C4 C5 UDP sing 439 n n 
C4 O4 UDP doub 440 n n 
C5 C6 UDP doub 441 n n 
C5 H5 UDP sing 442 n n 
C6 H6 UDP sing 443 n n 
C1' C2' UDP sing 444 n n 
C1' O4' UDP sing 445 n n 
C1' H1' UDP sing 446 n n 
C2' O2' UDP sing 447 n n 
C2' C3' UDP sing 448 n n 
C2' H2' UDP sing 449 n n 
O2' HO2' UDP sing 450 n n 
C3' C4' UDP sing 451 n n 
C3' O3' UDP sing 452 n n 
C3' H3' UDP sing 453 n n 
C4' O4' UDP sing 454 n n 
C4' C5' UDP sing 455 n n 
C4' H4' UDP sing 456 n n 
O3' HO3' UDP sing 457 n n 
C5' O5' UDP sing 458 n n 
C5' "H5'1" UDP sing 459 n n 
C5' "H5'2" UDP sing 460 n n 
O5' PA UDP sing 461 n n 
PA O1A UDP doub 462 n n 
PA O2A UDP sing 463 n n 
PA O3A UDP sing 464 n n 
O2A HOA2 UDP sing 465 n n 
O3A PB UDP sing 466 n n 
PB O1B UDP doub 467 n n 
PB O2B UDP sing 468 n n 
PB O3B UDP sing 469 n n 
O2B HOB2 UDP sing 470 n n 
O3B HOB3 UDP sing 471 n n 
#
_atom_sites.entry_id                     8B63 
_atom_sites.fract_transf_matrix[1][1]    0.023945 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000093 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009094 
_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]    0.010602 
_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 UD2 A 1 401 1 UD2 UD2 . 
D 3 ACT A 1 402 1 ACT ACT . 
E 4 UDP B 1 401 1 UDP UDP . 
F 5 HOH A 1 501 16 HOH HOH . 
F 5 HOH A 2 502 60 HOH HOH . 
F 5 HOH A 3 503 4 HOH HOH . 
F 5 HOH A 4 504 50 HOH HOH . 
F 5 HOH A 5 505 49 HOH HOH . 
F 5 HOH A 6 506 66 HOH HOH . 
F 5 HOH A 7 507 3 HOH HOH . 
F 5 HOH A 8 508 35 HOH HOH . 
F 5 HOH A 9 509 64 HOH HOH . 
F 5 HOH A 10 510 62 HOH HOH . 
F 5 HOH A 11 511 39 HOH HOH . 
F 5 HOH A 12 512 18 HOH HOH . 
F 5 HOH A 13 513 1 HOH HOH . 
F 5 HOH A 14 514 2 HOH HOH . 
F 5 HOH A 15 515 22 HOH HOH . 
F 5 HOH A 16 516 57 HOH HOH . 
F 5 HOH A 17 517 10 HOH HOH . 
F 5 HOH A 18 518 34 HOH HOH . 
F 5 HOH A 19 519 33 HOH HOH . 
F 5 HOH A 20 520 14 HOH HOH . 
F 5 HOH A 21 521 20 HOH HOH . 
F 5 HOH A 22 522 21 HOH HOH . 
F 5 HOH A 23 523 38 HOH HOH . 
F 5 HOH A 24 524 9 HOH HOH . 
F 5 HOH A 25 525 8 HOH HOH . 
F 5 HOH A 26 526 36 HOH HOH . 
F 5 HOH A 27 527 65 HOH HOH . 
F 5 HOH A 28 528 51 HOH HOH . 
F 5 HOH A 29 529 46 HOH HOH . 
F 5 HOH A 30 530 56 HOH HOH . 
F 5 HOH A 31 531 63 HOH HOH . 
F 5 HOH A 32 532 6 HOH HOH . 
F 5 HOH A 33 533 7 HOH HOH . 
F 5 HOH A 34 534 48 HOH HOH . 
F 5 HOH A 35 535 19 HOH HOH . 
F 5 HOH A 36 536 31 HOH HOH . 
F 5 HOH A 37 537 12 HOH HOH . 
F 5 HOH A 38 538 15 HOH HOH . 
F 5 HOH A 39 539 11 HOH HOH . 
F 5 HOH A 40 540 40 HOH HOH . 
F 5 HOH A 41 541 61 HOH HOH . 
F 5 HOH A 42 542 59 HOH HOH . 
F 5 HOH A 43 543 68 HOH HOH . 
F 5 HOH A 44 544 52 HOH HOH . 
F 5 HOH A 45 545 13 HOH HOH . 
F 5 HOH A 46 546 54 HOH HOH . 
F 5 HOH A 47 547 67 HOH HOH . 
F 5 HOH A 48 548 32 HOH HOH . 
F 5 HOH A 49 549 47 HOH HOH . 
F 5 HOH A 50 550 17 HOH HOH . 
F 5 HOH A 51 551 55 HOH HOH . 
F 5 HOH A 52 552 58 HOH HOH . 
G 5 HOH B 1 501 71 HOH HOH . 
G 5 HOH B 2 502 30 HOH HOH . 
G 5 HOH B 3 503 27 HOH HOH . 
G 5 HOH B 4 504 75 HOH HOH . 
G 5 HOH B 5 505 81 HOH HOH . 
G 5 HOH B 6 506 44 HOH HOH . 
G 5 HOH B 7 507 53 HOH HOH . 
G 5 HOH B 8 508 74 HOH HOH . 
G 5 HOH B 9 509 43 HOH HOH . 
G 5 HOH B 10 510 83 HOH HOH . 
G 5 HOH B 11 511 95 HOH HOH . 
G 5 HOH B 12 512 90 HOH HOH . 
G 5 HOH B 13 513 93 HOH HOH . 
G 5 HOH B 14 514 24 HOH HOH . 
G 5 HOH B 15 515 28 HOH HOH . 
G 5 HOH B 16 516 72 HOH HOH . 
G 5 HOH B 17 517 94 HOH HOH . 
G 5 HOH B 18 518 45 HOH HOH . 
G 5 HOH B 19 519 79 HOH HOH . 
G 5 HOH B 20 520 26 HOH HOH . 
G 5 HOH B 21 521 41 HOH HOH . 
G 5 HOH B 22 522 69 HOH HOH . 
G 5 HOH B 23 523 86 HOH HOH . 
G 5 HOH B 24 524 78 HOH HOH . 
G 5 HOH B 25 525 82 HOH HOH . 
G 5 HOH B 26 526 89 HOH HOH . 
G 5 HOH B 27 527 91 HOH HOH . 
G 5 HOH B 28 528 77 HOH HOH . 
G 5 HOH B 29 529 23 HOH HOH . 
G 5 HOH B 30 530 85 HOH HOH . 
G 5 HOH B 31 531 25 HOH HOH . 
G 5 HOH B 32 532 80 HOH HOH . 
G 5 HOH B 33 533 88 HOH HOH . 
G 5 HOH B 34 534 42 HOH HOH . 
G 5 HOH B 35 535 73 HOH HOH . 
G 5 HOH B 36 536 76 HOH HOH . 
G 5 HOH B 37 537 92 HOH HOH . 
G 5 HOH B 38 538 84 HOH HOH . 
G 5 HOH B 39 539 96 HOH HOH . 
G 5 HOH B 40 540 70 HOH HOH . 
G 5 HOH B 41 541 29 HOH HOH . 
G 5 HOH B 42 542 87 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 4 19.785 40.961 21.183 1 35.52 ? N1 UDP 401 B 1 
HETATM 2 C C2 UDP . . . E 4 20.48 40.382 22.243 1 35.43 ? C2 UDP 401 B 1 
HETATM 3 N N3 UDP . . . E 4 21.386 41.221 22.844 1 32.14 ? N3 UDP 401 B 1 
HETATM 4 C C4 UDP . . . E 4 21.665 42.538 22.515 1 33.96 ? C4 UDP 401 B 1 
HETATM 5 C C5 UDP . . . E 4 20.912 43.055 21.421 1 30.01 ? C5 UDP 401 B 1 
HETATM 6 C C6 UDP . . . E 4 20.005 42.272 20.816 1 33.98 ? C6 UDP 401 B 1 
HETATM 7 O O2 UDP . . . E 4 20.303 39.224 22.624 1 29.22 ? O2 UDP 401 B 1 
HETATM 8 O O4 UDP . . . E 4 22.49 43.184 23.173 1 34.94 ? O4 UDP 401 B 1 
HETATM 9 C C1' UDP . . . E 4 18.778 40.15 20.473 1 32.23 ? C1' UDP 401 B 1 
HETATM 10 C C2' UDP . . . E 4 17.378 40.753 20.541 1 35.25 ? C2' UDP 401 B 1 
HETATM 11 O O2' UDP . . . E 4 16.831 40.511 21.822 1 34.1 ? O2' UDP 401 B 1 
HETATM 12 C C3' UDP . . . E 4 16.751 40.005 19.349 1 35.13 ? C3' UDP 401 B 1 
HETATM 13 C C4' UDP . . . E 4 17.873 40.082 18.301 1 31.85 ? C4' UDP 401 B 1 
HETATM 14 O O4' UDP . . . E 4 19.088 40.139 19.097 1 34.9 ? O4' UDP 401 B 1 
HETATM 15 O O3' UDP . . . E 4 16.466 38.647 19.69 1 34.9 ? O3' UDP 401 B 1 
HETATM 16 C C5' UDP . . . E 4 17.857 41.251 17.342 1 32.68 ? C5' UDP 401 B 1 
HETATM 17 O O5' UDP . . . E 4 16.865 41.02 16.288 1 28.61 ? O5' UDP 401 B 1 
HETATM 18 P PA UDP . . . E 4 16.036 42.212 15.606 1 32.71 ? PA UDP 401 B 1 
HETATM 19 O O1A UDP . . . E 4 15.101 41.61 14.614 1 29.71 ? O1A UDP 401 B 1 
HETATM 20 O O2A UDP . . . E 4 15.451 43.138 16.654 1 30.23 ? O2A UDP 401 B 1 
HETATM 21 O O3A UDP . . . E 4 17.161 43.125 14.882 1 35.6 ? O3A UDP 401 B 1 
HETATM 22 P PB UDP . . . E 4 18.312 42.827 13.805 1 37.85 ? PB UDP 401 B 1 
HETATM 23 O O1B UDP . . . E 4 17.775 41.634 13.017 1 32.28 ? O1B UDP 401 B 1 
HETATM 24 O O2B UDP . . . E 4 18.434 44.087 13.085 1 32.93 ? O2B UDP 401 B 1 
HETATM 25 O O3B UDP . . . E 4 19.604 42.479 14.562 1 43.89 ? O3B UDP 401 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           221 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#