data_4XSP
#
_model_server_result.job_id            UCDG8_cA_bHKLbetHvPHPQ 
_model_server_result.datetime_utc      '2025-07-15 13:59:52' 
_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          4xsp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    4XSP 
#
_exptl.entry_id    4XSP 
_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    1 
_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            4XSP 
_cell.length_a            78.883 
_cell.length_b            133.223 
_cell.length_c            143.019 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XSP 
_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 
_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                      3 
_struct_asym.id                             D 
_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 371 n n 
N1 C6 UDP sing 372 n n 
N1 C1' UDP sing 373 n n 
C2 N3 UDP sing 374 n n 
C2 O2 UDP doub 375 n n 
N3 C4 UDP sing 376 n n 
N3 HN3 UDP sing 377 n n 
C4 C5 UDP sing 378 n n 
C4 O4 UDP doub 379 n n 
C5 C6 UDP doub 380 n n 
C5 H5 UDP sing 381 n n 
C6 H6 UDP sing 382 n n 
C1' C2' UDP sing 383 n n 
C1' O4' UDP sing 384 n n 
C1' H1' UDP sing 385 n n 
C2' O2' UDP sing 386 n n 
C2' C3' UDP sing 387 n n 
C2' H2' UDP sing 388 n n 
O2' HO2' UDP sing 389 n n 
C3' C4' UDP sing 390 n n 
C3' O3' UDP sing 391 n n 
C3' H3' UDP sing 392 n n 
C4' O4' UDP sing 393 n n 
C4' C5' UDP sing 394 n n 
C4' H4' UDP sing 395 n n 
O3' HO3' UDP sing 396 n n 
C5' O5' UDP sing 397 n n 
C5' "H5'1" UDP sing 398 n n 
C5' "H5'2" UDP sing 399 n n 
O5' PA UDP sing 400 n n 
PA O1A UDP doub 401 n n 
PA O2A UDP sing 402 n n 
PA O3A UDP sing 403 n n 
O2A HOA2 UDP sing 404 n n 
O3A PB UDP sing 405 n n 
PB O1B UDP doub 406 n n 
PB O2B UDP sing 407 n n 
PB O3B UDP sing 408 n n 
O2B HOB2 UDP sing 409 n n 
O3B HOB3 UDP sing 410 n n 
#
_atom_sites.entry_id                     4XSP 
_atom_sites.fract_transf_matrix[1][1]    0.012677 
_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]    0.007506 
_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]    0.006992 
_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 GOL B 1 401 401 GOL GOL . 
D 3 UDP A 1 401 401 UDP UDP . 
E 2 GOL A 1 402 402 GOL GOL . 
F 4 HOH B 1 501 501 HOH HOH . 
F 4 HOH B 2 502 503 HOH HOH . 
F 4 HOH B 3 503 505 HOH HOH . 
F 4 HOH B 4 504 502 HOH HOH . 
F 4 HOH B 5 505 504 HOH HOH . 
F 4 HOH B 6 506 507 HOH HOH . 
F 4 HOH B 7 507 508 HOH HOH . 
F 4 HOH B 8 508 510 HOH HOH . 
F 4 HOH B 9 509 511 HOH HOH . 
F 4 HOH B 10 510 506 HOH HOH . 
F 4 HOH B 11 511 509 HOH HOH . 
F 4 HOH B 12 512 513 HOH HOH . 
F 4 HOH B 13 513 512 HOH HOH . 
F 4 HOH B 14 514 514 HOH HOH . 
F 4 HOH B 15 515 516 HOH HOH . 
F 4 HOH B 16 516 515 HOH HOH . 
F 4 HOH B 17 517 518 HOH HOH . 
F 4 HOH B 18 518 517 HOH HOH . 
F 4 HOH B 19 519 520 HOH HOH . 
F 4 HOH B 20 520 519 HOH HOH . 
F 4 HOH B 21 521 521 HOH HOH . 
F 4 HOH B 22 522 522 HOH HOH . 
F 4 HOH B 23 523 524 HOH HOH . 
F 4 HOH B 24 524 523 HOH HOH . 
F 4 HOH B 25 525 524 HOH HOH . 
F 4 HOH B 26 526 525 HOH HOH . 
F 4 HOH B 27 527 526 HOH HOH . 
F 4 HOH B 28 528 527 HOH HOH . 
F 4 HOH B 29 529 528 HOH HOH . 
F 4 HOH B 30 530 529 HOH HOH . 
F 4 HOH B 31 531 530 HOH HOH . 
F 4 HOH B 32 532 531 HOH HOH . 
F 4 HOH B 33 533 532 HOH HOH . 
F 4 HOH B 34 534 533 HOH HOH . 
F 4 HOH B 35 535 534 HOH HOH . 
F 4 HOH B 36 536 535 HOH HOH . 
F 4 HOH B 37 537 536 HOH HOH . 
F 4 HOH B 38 538 537 HOH HOH . 
F 4 HOH B 39 539 538 HOH HOH . 
F 4 HOH B 40 540 539 HOH HOH . 
F 4 HOH B 41 541 540 HOH HOH . 
F 4 HOH B 42 542 541 HOH HOH . 
F 4 HOH B 43 543 542 HOH HOH . 
F 4 HOH B 44 544 543 HOH HOH . 
F 4 HOH B 45 545 544 HOH HOH . 
F 4 HOH B 46 546 545 HOH HOH . 
F 4 HOH B 47 547 546 HOH HOH . 
F 4 HOH B 48 548 547 HOH HOH . 
F 4 HOH B 49 549 548 HOH HOH . 
F 4 HOH B 50 550 549 HOH HOH . 
F 4 HOH B 51 551 550 HOH HOH . 
F 4 HOH B 52 552 551 HOH HOH . 
F 4 HOH B 53 553 552 HOH HOH . 
F 4 HOH B 54 554 553 HOH HOH . 
F 4 HOH B 55 555 554 HOH HOH . 
F 4 HOH B 56 556 555 HOH HOH . 
F 4 HOH B 57 557 556 HOH HOH . 
F 4 HOH B 58 558 557 HOH HOH . 
F 4 HOH B 59 559 558 HOH HOH . 
F 4 HOH B 60 560 559 HOH HOH . 
F 4 HOH B 61 561 560 HOH HOH . 
F 4 HOH B 62 562 561 HOH HOH . 
F 4 HOH B 63 563 562 HOH HOH . 
F 4 HOH B 64 564 563 HOH HOH . 
F 4 HOH B 65 565 564 HOH HOH . 
F 4 HOH B 66 566 565 HOH HOH . 
F 4 HOH B 67 567 566 HOH HOH . 
F 4 HOH B 68 568 567 HOH HOH . 
F 4 HOH B 69 569 568 HOH HOH . 
F 4 HOH B 70 570 569 HOH HOH . 
F 4 HOH B 71 571 570 HOH HOH . 
F 4 HOH B 72 572 571 HOH HOH . 
F 4 HOH B 73 573 572 HOH HOH . 
F 4 HOH B 74 574 573 HOH HOH . 
F 4 HOH B 75 575 574 HOH HOH . 
F 4 HOH B 76 576 575 HOH HOH . 
F 4 HOH B 77 577 576 HOH HOH . 
G 4 HOH A 1 501 502 HOH HOH . 
G 4 HOH A 2 502 501 HOH HOH . 
G 4 HOH A 3 503 514 HOH HOH . 
G 4 HOH A 4 504 508 HOH HOH . 
G 4 HOH A 5 505 503 HOH HOH . 
G 4 HOH A 6 506 504 HOH HOH . 
G 4 HOH A 7 507 505 HOH HOH . 
G 4 HOH A 8 508 510 HOH HOH . 
G 4 HOH A 9 509 509 HOH HOH . 
G 4 HOH A 10 510 506 HOH HOH . 
G 4 HOH A 11 511 507 HOH HOH . 
G 4 HOH A 12 512 511 HOH HOH . 
G 4 HOH A 13 513 512 HOH HOH . 
G 4 HOH A 14 514 513 HOH HOH . 
G 4 HOH A 15 515 515 HOH HOH . 
G 4 HOH A 16 516 519 HOH HOH . 
G 4 HOH A 17 517 522 HOH HOH . 
G 4 HOH A 18 518 516 HOH HOH . 
G 4 HOH A 19 519 521 HOH HOH . 
G 4 HOH A 20 520 520 HOH HOH . 
G 4 HOH A 21 521 517 HOH HOH . 
G 4 HOH A 22 522 518 HOH HOH . 
G 4 HOH A 23 523 523 HOH HOH . 
G 4 HOH A 24 524 525 HOH HOH . 
G 4 HOH A 25 525 526 HOH HOH . 
G 4 HOH A 26 526 527 HOH HOH . 
G 4 HOH A 27 527 528 HOH HOH . 
G 4 HOH A 28 528 529 HOH HOH . 
G 4 HOH A 29 529 530 HOH HOH . 
G 4 HOH A 30 530 531 HOH HOH . 
G 4 HOH A 31 531 532 HOH HOH . 
G 4 HOH A 32 532 533 HOH HOH . 
G 4 HOH A 33 533 534 HOH HOH . 
G 4 HOH A 34 534 535 HOH HOH . 
G 4 HOH A 35 535 536 HOH HOH . 
G 4 HOH A 36 536 537 HOH HOH . 
G 4 HOH A 37 537 538 HOH HOH . 
G 4 HOH A 38 538 539 HOH HOH . 
G 4 HOH A 39 539 540 HOH HOH . 
G 4 HOH A 40 540 541 HOH HOH . 
G 4 HOH A 41 541 542 HOH HOH . 
G 4 HOH A 42 542 543 HOH HOH . 
G 4 HOH A 43 543 544 HOH HOH . 
G 4 HOH A 44 544 545 HOH HOH . 
G 4 HOH A 45 545 546 HOH HOH . 
G 4 HOH A 46 546 547 HOH HOH . 
G 4 HOH A 47 547 548 HOH HOH . 
G 4 HOH A 48 548 549 HOH HOH . 
G 4 HOH A 49 549 550 HOH HOH . 
G 4 HOH A 50 550 551 HOH HOH . 
G 4 HOH A 51 551 552 HOH HOH . 
G 4 HOH A 52 552 553 HOH HOH . 
G 4 HOH A 53 553 554 HOH HOH . 
G 4 HOH A 54 554 555 HOH HOH . 
G 4 HOH A 55 555 556 HOH HOH . 
G 4 HOH A 56 556 557 HOH HOH . 
G 4 HOH A 57 557 558 HOH HOH . 
G 4 HOH A 58 558 559 HOH HOH . 
G 4 HOH A 59 559 560 HOH HOH . 
G 4 HOH A 60 560 561 HOH HOH . 
G 4 HOH A 61 561 562 HOH HOH . 
G 4 HOH A 62 562 563 HOH HOH . 
G 4 HOH A 63 563 564 HOH HOH . 
G 4 HOH A 64 564 565 HOH HOH . 
G 4 HOH A 65 565 566 HOH HOH . 
G 4 HOH A 66 566 567 HOH HOH . 
G 4 HOH A 67 567 568 HOH HOH . 
G 4 HOH A 68 568 569 HOH HOH . 
G 4 HOH A 69 569 570 HOH HOH . 
G 4 HOH A 70 570 571 HOH HOH . 
G 4 HOH A 71 571 572 HOH HOH . 
G 4 HOH A 72 572 573 HOH HOH . 
G 4 HOH A 73 573 574 HOH HOH . 
G 4 HOH A 74 574 575 HOH HOH . 
G 4 HOH A 75 575 576 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 . . . D 3 22.753 31.625 11.433 1 33.88 ? N1 UDP 401 A 1 
HETATM 2 C C2 UDP . . . D 3 23.718 31.825 10.428 1 35.9 ? C2 UDP 401 A 1 
HETATM 3 N N3 UDP . . . D 3 23.384 32.427 9.272 1 41.5 ? N3 UDP 401 A 1 
HETATM 4 C C4 UDP . . . D 3 22.108 32.817 9.035 1 41.73 ? C4 UDP 401 A 1 
HETATM 5 C C5 UDP . . . D 3 21.118 32.609 10.004 1 38.44 ? C5 UDP 401 A 1 
HETATM 6 C C6 UDP . . . D 3 21.479 32.007 11.212 1 37.07 ? C6 UDP 401 A 1 
HETATM 7 O O2 UDP . . . D 3 24.907 31.475 10.583 1 36.96 ? O2 UDP 401 A 1 
HETATM 8 O O4 UDP . . . D 3 21.839 33.36 7.943 1 40.35 ? O4 UDP 401 A 1 
HETATM 9 C C1' UDP . . . D 3 23.127 30.99 12.71 1 36.57 ? C1' UDP 401 A 1 
HETATM 10 C C2' UDP . . . D 3 22.958 31.888 13.945 1 37.66 ? C2' UDP 401 A 1 
HETATM 11 O O2' UDP . . . D 3 24.055 32.812 14.107 1 32.54 ? O2' UDP 401 A 1 
HETATM 12 C C3' UDP . . . D 3 22.87 30.869 15.069 1 38.32 ? C3' UDP 401 A 1 
HETATM 13 C C4' UDP . . . D 3 22.177 29.676 14.396 1 38.19 ? C4' UDP 401 A 1 
HETATM 14 O O4' UDP . . . D 3 22.335 29.842 13.017 1 37.09 ? O4' UDP 401 A 1 
HETATM 15 O O3' UDP . . . D 3 24.2 30.537 15.523 1 37.19 ? O3' UDP 401 A 1 
HETATM 16 C C5' UDP . . . D 3 20.675 29.645 14.629 1 37.04 ? C5' UDP 401 A 1 
HETATM 17 O O5' UDP . . . D 3 20.523 29.247 15.978 1 36.94 ? O5' UDP 401 A 1 
HETATM 18 P PA UDP . . . D 3 19.18 29.465 16.823 1 39.38 ? PA UDP 401 A 1 
HETATM 19 O O1A UDP . . . D 3 18.978 30.968 16.976 1 41.76 ? O1A UDP 401 A 1 
HETATM 20 O O2A UDP . . . D 3 19.41 28.731 18.121 1 36.47 ? O2A UDP 401 A 1 
HETATM 21 O O3A UDP . . . D 3 18.018 28.822 15.869 1 47.49 ? O3A UDP 401 A 1 
HETATM 22 P PB UDP . . . D 3 17.425 27.29 15.906 1 52.82 ? PB UDP 401 A 1 
HETATM 23 O O1B UDP . . . D 3 16.134 27.404 15.159 1 58.36 ? O1B UDP 401 A 1 
HETATM 24 O O2B UDP . . . D 3 17.21 27.008 17.378 1 56.98 ? O2B UDP 401 A 1 
HETATM 25 O O3B UDP . . . D 3 18.487 26.472 15.221 1 52.8 ? O3B UDP 401 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           382 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#