data_3INT
#
_model_server_result.job_id            26oNzb5Ro_KXER5mA7k9qQ 
_model_server_result.datetime_utc      '2024-11-15 02:49:26' 
_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          3int 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":392}' 
#
_entry.id    3INT 
#
_exptl.entry_id    3INT 
_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            3INT 
_cell.length_a            94.078 
_cell.length_b            94.078 
_cell.length_c            129.443 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3INT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 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,C,D,E,F,G,H 1 1 
A,C,D,G 2 1 
B,E,F,H 3 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 513 n n 
N1 C6 UDP sing 514 n n 
N1 C1' UDP sing 515 n n 
C2 N3 UDP sing 516 n n 
C2 O2 UDP doub 517 n n 
N3 C4 UDP sing 518 n n 
N3 HN3 UDP sing 519 n n 
C4 C5 UDP sing 520 n n 
C4 O4 UDP doub 521 n n 
C5 C6 UDP doub 522 n n 
C5 H5 UDP sing 523 n n 
C6 H6 UDP sing 524 n n 
C1' C2' UDP sing 525 n n 
C1' O4' UDP sing 526 n n 
C1' H1' UDP sing 527 n n 
C2' O2' UDP sing 528 n n 
C2' C3' UDP sing 529 n n 
C2' H2' UDP sing 530 n n 
O2' HO2' UDP sing 531 n n 
C3' C4' UDP sing 532 n n 
C3' O3' UDP sing 533 n n 
C3' H3' UDP sing 534 n n 
C4' O4' UDP sing 535 n n 
C4' C5' UDP sing 536 n n 
C4' H4' UDP sing 537 n n 
O3' HO3' UDP sing 538 n n 
C5' O5' UDP sing 539 n n 
C5' "H5'1" UDP sing 540 n n 
C5' "H5'2" UDP sing 541 n n 
O5' PA UDP sing 542 n n 
PA O1A UDP doub 543 n n 
PA O2A UDP sing 544 n n 
PA O3A UDP sing 545 n n 
O2A HOA2 UDP sing 546 n n 
O3A PB UDP sing 547 n n 
PB O1B UDP doub 548 n n 
PB O2B UDP sing 549 n n 
PB O3B UDP sing 550 n n 
O2B HOB2 UDP sing 551 n n 
O3B HOB3 UDP sing 552 n n 
#
_atom_sites.entry_id                     3INT 
_atom_sites.fract_transf_matrix[1][1]    0.010629 
_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]    0.010629 
_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]    0.007725 
_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 FDA A 1 391 385 FDA FDA . 
D 3 UDP A 1 392 387 UDP UDP . 
E 2 FDA B 1 391 386 FDA FDA . 
F 4 GDU B 1 392 388 GDU GDU . 
G 5 HOH A 1 393 389 HOH HOH . 
G 5 HOH A 2 394 394 HOH HOH . 
G 5 HOH A 3 395 395 HOH HOH . 
G 5 HOH A 4 396 396 HOH HOH . 
G 5 HOH A 5 397 390 HOH HOH . 
G 5 HOH A 6 398 398 HOH HOH . 
G 5 HOH A 7 399 392 HOH HOH . 
G 5 HOH A 8 400 400 HOH HOH . 
G 5 HOH A 9 401 401 HOH HOH . 
G 5 HOH A 10 402 402 HOH HOH . 
G 5 HOH A 11 403 403 HOH HOH . 
G 5 HOH A 12 404 404 HOH HOH . 
G 5 HOH A 13 408 408 HOH HOH . 
G 5 HOH A 14 409 409 HOH HOH . 
G 5 HOH A 15 410 410 HOH HOH . 
G 5 HOH A 16 413 413 HOH HOH . 
G 5 HOH A 17 414 414 HOH HOH . 
G 5 HOH A 18 418 418 HOH HOH . 
G 5 HOH A 19 420 420 HOH HOH . 
G 5 HOH A 20 421 421 HOH HOH . 
G 5 HOH A 21 422 422 HOH HOH . 
G 5 HOH A 22 426 426 HOH HOH . 
G 5 HOH A 23 429 429 HOH HOH . 
G 5 HOH A 24 431 431 HOH HOH . 
G 5 HOH A 25 432 432 HOH HOH . 
G 5 HOH A 26 434 434 HOH HOH . 
G 5 HOH A 27 435 435 HOH HOH . 
G 5 HOH A 28 438 438 HOH HOH . 
G 5 HOH A 29 439 439 HOH HOH . 
G 5 HOH A 30 440 440 HOH HOH . 
G 5 HOH A 31 441 441 HOH HOH . 
G 5 HOH A 32 442 442 HOH HOH . 
G 5 HOH A 33 443 443 HOH HOH . 
G 5 HOH A 34 444 444 HOH HOH . 
G 5 HOH A 35 445 445 HOH HOH . 
G 5 HOH A 36 452 452 HOH HOH . 
G 5 HOH A 37 453 453 HOH HOH . 
G 5 HOH A 38 455 455 HOH HOH . 
G 5 HOH A 39 456 456 HOH HOH . 
G 5 HOH A 40 459 459 HOH HOH . 
G 5 HOH A 41 461 461 HOH HOH . 
G 5 HOH A 42 462 462 HOH HOH . 
G 5 HOH A 43 465 465 HOH HOH . 
G 5 HOH A 44 467 467 HOH HOH . 
G 5 HOH A 45 470 470 HOH HOH . 
G 5 HOH A 46 471 471 HOH HOH . 
G 5 HOH A 47 472 472 HOH HOH . 
G 5 HOH A 48 473 473 HOH HOH . 
G 5 HOH A 49 474 474 HOH HOH . 
G 5 HOH A 50 475 475 HOH HOH . 
G 5 HOH A 51 477 477 HOH HOH . 
G 5 HOH A 52 481 481 HOH HOH . 
G 5 HOH A 53 483 483 HOH HOH . 
G 5 HOH A 54 484 484 HOH HOH . 
G 5 HOH A 55 488 488 HOH HOH . 
G 5 HOH A 56 489 489 HOH HOH . 
G 5 HOH A 57 492 492 HOH HOH . 
G 5 HOH A 58 493 493 HOH HOH . 
G 5 HOH A 59 494 494 HOH HOH . 
G 5 HOH A 60 496 496 HOH HOH . 
G 5 HOH A 61 498 498 HOH HOH . 
G 5 HOH A 62 499 499 HOH HOH . 
G 5 HOH A 63 501 501 HOH HOH . 
G 5 HOH A 64 502 502 HOH HOH . 
G 5 HOH A 65 505 505 HOH HOH . 
G 5 HOH A 66 508 508 HOH HOH . 
G 5 HOH A 67 510 510 HOH HOH . 
G 5 HOH A 68 513 513 HOH HOH . 
G 5 HOH A 69 515 515 HOH HOH . 
G 5 HOH A 70 517 517 HOH HOH . 
G 5 HOH A 71 518 518 HOH HOH . 
G 5 HOH A 72 519 519 HOH HOH . 
G 5 HOH A 73 520 520 HOH HOH . 
G 5 HOH A 74 521 521 HOH HOH . 
G 5 HOH A 75 524 524 HOH HOH . 
G 5 HOH A 76 525 525 HOH HOH . 
G 5 HOH A 77 527 527 HOH HOH . 
G 5 HOH A 78 531 531 HOH HOH . 
G 5 HOH A 79 533 533 HOH HOH . 
G 5 HOH A 80 535 535 HOH HOH . 
G 5 HOH A 81 538 538 HOH HOH . 
G 5 HOH A 82 539 539 HOH HOH . 
G 5 HOH A 83 546 546 HOH HOH . 
G 5 HOH A 84 549 549 HOH HOH . 
G 5 HOH A 85 550 550 HOH HOH . 
G 5 HOH A 86 551 551 HOH HOH . 
G 5 HOH A 87 552 552 HOH HOH . 
G 5 HOH A 88 553 553 HOH HOH . 
G 5 HOH A 89 554 554 HOH HOH . 
G 5 HOH A 90 555 555 HOH HOH . 
G 5 HOH A 91 557 557 HOH HOH . 
G 5 HOH A 92 558 558 HOH HOH . 
G 5 HOH A 93 560 560 HOH HOH . 
G 5 HOH A 94 561 561 HOH HOH . 
G 5 HOH A 95 562 562 HOH HOH . 
G 5 HOH A 96 563 563 HOH HOH . 
G 5 HOH A 97 568 568 HOH HOH . 
G 5 HOH A 98 578 578 HOH HOH . 
G 5 HOH A 99 579 579 HOH HOH . 
G 5 HOH A 100 580 580 HOH HOH . 
G 5 HOH A 101 581 581 HOH HOH . 
G 5 HOH A 102 582 582 HOH HOH . 
G 5 HOH A 103 583 583 HOH HOH . 
G 5 HOH A 104 584 584 HOH HOH . 
H 5 HOH B 1 393 393 HOH HOH . 
H 5 HOH B 2 394 391 HOH HOH . 
H 5 HOH B 3 397 397 HOH HOH . 
H 5 HOH B 4 399 399 HOH HOH . 
H 5 HOH B 5 405 405 HOH HOH . 
H 5 HOH B 6 406 406 HOH HOH . 
H 5 HOH B 7 407 407 HOH HOH . 
H 5 HOH B 8 411 411 HOH HOH . 
H 5 HOH B 9 412 412 HOH HOH . 
H 5 HOH B 10 415 415 HOH HOH . 
H 5 HOH B 11 416 416 HOH HOH . 
H 5 HOH B 12 417 417 HOH HOH . 
H 5 HOH B 13 419 419 HOH HOH . 
H 5 HOH B 14 423 423 HOH HOH . 
H 5 HOH B 15 424 424 HOH HOH . 
H 5 HOH B 16 425 425 HOH HOH . 
H 5 HOH B 17 427 427 HOH HOH . 
H 5 HOH B 18 428 428 HOH HOH . 
H 5 HOH B 19 430 430 HOH HOH . 
H 5 HOH B 20 433 433 HOH HOH . 
H 5 HOH B 21 436 436 HOH HOH . 
H 5 HOH B 22 437 437 HOH HOH . 
H 5 HOH B 23 446 446 HOH HOH . 
H 5 HOH B 24 447 447 HOH HOH . 
H 5 HOH B 25 448 448 HOH HOH . 
H 5 HOH B 26 449 449 HOH HOH . 
H 5 HOH B 27 450 450 HOH HOH . 
H 5 HOH B 28 451 451 HOH HOH . 
H 5 HOH B 29 454 454 HOH HOH . 
H 5 HOH B 30 457 457 HOH HOH . 
H 5 HOH B 31 458 458 HOH HOH . 
H 5 HOH B 32 460 460 HOH HOH . 
H 5 HOH B 33 463 463 HOH HOH . 
H 5 HOH B 34 464 464 HOH HOH . 
H 5 HOH B 35 466 466 HOH HOH . 
H 5 HOH B 36 468 468 HOH HOH . 
H 5 HOH B 37 469 469 HOH HOH . 
H 5 HOH B 38 476 476 HOH HOH . 
H 5 HOH B 39 478 478 HOH HOH . 
H 5 HOH B 40 479 479 HOH HOH . 
H 5 HOH B 41 480 480 HOH HOH . 
H 5 HOH B 42 482 482 HOH HOH . 
H 5 HOH B 43 485 485 HOH HOH . 
H 5 HOH B 44 486 486 HOH HOH . 
H 5 HOH B 45 487 487 HOH HOH . 
H 5 HOH B 46 490 490 HOH HOH . 
H 5 HOH B 47 491 491 HOH HOH . 
H 5 HOH B 48 495 495 HOH HOH . 
H 5 HOH B 49 497 497 HOH HOH . 
H 5 HOH B 50 500 500 HOH HOH . 
H 5 HOH B 51 503 503 HOH HOH . 
H 5 HOH B 52 504 504 HOH HOH . 
H 5 HOH B 53 506 506 HOH HOH . 
H 5 HOH B 54 507 507 HOH HOH . 
H 5 HOH B 55 509 509 HOH HOH . 
H 5 HOH B 56 511 511 HOH HOH . 
H 5 HOH B 57 512 512 HOH HOH . 
H 5 HOH B 58 514 514 HOH HOH . 
H 5 HOH B 59 516 516 HOH HOH . 
H 5 HOH B 60 522 522 HOH HOH . 
H 5 HOH B 61 523 523 HOH HOH . 
H 5 HOH B 62 526 526 HOH HOH . 
H 5 HOH B 63 528 528 HOH HOH . 
H 5 HOH B 64 529 529 HOH HOH . 
H 5 HOH B 65 530 530 HOH HOH . 
H 5 HOH B 66 532 532 HOH HOH . 
H 5 HOH B 67 534 534 HOH HOH . 
H 5 HOH B 68 536 536 HOH HOH . 
H 5 HOH B 69 537 537 HOH HOH . 
H 5 HOH B 70 540 540 HOH HOH . 
H 5 HOH B 71 541 541 HOH HOH . 
H 5 HOH B 72 542 542 HOH HOH . 
H 5 HOH B 73 543 543 HOH HOH . 
H 5 HOH B 74 544 544 HOH HOH . 
H 5 HOH B 75 545 545 HOH HOH . 
H 5 HOH B 76 547 547 HOH HOH . 
H 5 HOH B 77 548 548 HOH HOH . 
H 5 HOH B 78 556 556 HOH HOH . 
H 5 HOH B 79 559 559 HOH HOH . 
H 5 HOH B 80 564 564 HOH HOH . 
H 5 HOH B 81 565 565 HOH HOH . 
H 5 HOH B 82 566 566 HOH HOH . 
H 5 HOH B 83 567 567 HOH HOH . 
H 5 HOH B 84 569 569 HOH HOH . 
H 5 HOH B 85 570 570 HOH HOH . 
H 5 HOH B 86 571 571 HOH HOH . 
H 5 HOH B 87 572 572 HOH HOH . 
H 5 HOH B 88 573 573 HOH HOH . 
H 5 HOH B 89 574 574 HOH HOH . 
H 5 HOH B 90 575 575 HOH HOH . 
H 5 HOH B 91 576 576 HOH HOH . 
H 5 HOH B 92 577 577 HOH HOH . 
H 5 HOH B 93 585 585 HOH HOH . 
H 5 HOH B 94 586 586 HOH HOH . 
H 5 HOH B 95 587 587 HOH HOH . 
H 5 HOH B 96 588 588 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 -9.29 -19.08 3.887 1 29.7 ? N1 UDP 392 A 1 
HETATM 2 C C2 UDP . . . D 3 -10.49 -19.005 4.542 1 27.7 ? C2 UDP 392 A 1 
HETATM 3 N N3 UDP . . . D 3 -10.918 -20.039 5.301 1 27.51 ? N3 UDP 392 A 1 
HETATM 4 C C4 UDP . . . D 3 -10.176 -21.193 5.452 1 28.56 ? C4 UDP 392 A 1 
HETATM 5 C C5 UDP . . . D 3 -8.936 -21.299 4.796 1 27.87 ? C5 UDP 392 A 1 
HETATM 6 C C6 UDP . . . D 3 -8.471 -20.194 4.062 1 29.04 ? C6 UDP 392 A 1 
HETATM 7 O O2 UDP . . . D 3 -11.201 -18.015 4.474 1 33.24 ? O2 UDP 392 A 1 
HETATM 8 O O4 UDP . . . D 3 -10.657 -22.062 6.199 1 24.33 ? O4 UDP 392 A 1 
HETATM 9 C C1' UDP . . . D 3 -8.905 -17.913 3.089 1 28.4 ? C1' UDP 392 A 1 
HETATM 10 C C2' UDP . . . D 3 -8.163 -17 4.028 1 31.08 ? C2' UDP 392 A 1 
HETATM 11 O O2' UDP . . . D 3 -8.556 -15.661 3.791 1 26.75 ? O2' UDP 392 A 1 
HETATM 12 C C3' UDP . . . D 3 -6.711 -17.272 3.668 1 32.69 ? C3' UDP 392 A 1 
HETATM 13 C C4' UDP . . . D 3 -6.781 -17.636 2.189 1 33.96 ? C4' UDP 392 A 1 
HETATM 14 O O4' UDP . . . D 3 -8.019 -18.256 2.059 1 30.16 ? O4' UDP 392 A 1 
HETATM 15 O O3' UDP . . . D 3 -5.911 -16.143 3.9 1 32.23 ? O3' UDP 392 A 1 
HETATM 16 C C5' UDP . . . D 3 -5.698 -18.579 1.637 1 39.33 ? C5' UDP 392 A 1 
HETATM 17 O O5' UDP . . . D 3 -5.367 -19.471 2.682 1 42.92 ? O5' UDP 392 A 1 
HETATM 18 P PA UDP . . . D 3 -4.376 -20.719 2.621 1 41.25 ? PA UDP 392 A 1 
HETATM 19 O O1A UDP . . . D 3 -5.001 -21.676 1.729 1 45.05 ? O1A UDP 392 A 1 
HETATM 20 O O2A UDP . . . D 3 -4.264 -21.22 3.994 1 38.16 ? O2A UDP 392 A 1 
HETATM 21 O O3A UDP . . . D 3 -2.996 -20.423 1.832 1 49.92 ? O3A UDP 392 A 1 
HETATM 22 P PB UDP . . . D 3 -1.733 -19.61 2.508 1 59.89 ? PB UDP 392 A 1 
HETATM 23 O O1B UDP . . . D 3 -2.22 -19.096 3.834 1 55.78 ? O1B UDP 392 A 1 
HETATM 24 O O2B UDP . . . D 3 -1.341 -18.566 1.468 1 60.98 ? O2B UDP 392 A 1 
HETATM 25 O O3B UDP . . . D 3 -0.489 -20.388 2.792 1 57.82 ? O3B UDP 392 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#