data_3GF4
#
_model_server_result.job_id            Thn84OoiHsG_WEVEpHKRVQ 
_model_server_result.datetime_utc      '2024-11-24 17:45:26' 
_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          3gf4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":392}' 
#
_entry.id    3GF4 
#
_exptl.entry_id    3GF4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_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            3GF4 
_cell.length_a            93.951 
_cell.length_b            93.951 
_cell.length_c            130.259 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GF4 
_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 
B,E,F,H 2 1 
A,C,D,G 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                      4 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 U5P sing 449 n n 
N1 C6 U5P sing 450 n n 
N1 C1' U5P sing 451 n n 
C2 N3 U5P sing 452 n n 
C2 O2 U5P doub 453 n n 
N3 C4 U5P sing 454 n n 
N3 HN3 U5P sing 455 n n 
C4 C5 U5P sing 456 n n 
C4 O4 U5P doub 457 n n 
C5 C6 U5P doub 458 n n 
C5 H5 U5P sing 459 n n 
C6 H6 U5P sing 460 n n 
C1' C2' U5P sing 461 n n 
C1' O4' U5P sing 462 n n 
C1' H1' U5P sing 463 n n 
C2' O2' U5P sing 464 n n 
C2' C3' U5P sing 465 n n 
C2' H2' U5P sing 466 n n 
O2' HO2' U5P sing 467 n n 
C3' C4' U5P sing 468 n n 
C3' O3' U5P sing 469 n n 
C3' H3' U5P sing 470 n n 
C4' O4' U5P sing 471 n n 
C4' C5' U5P sing 472 n n 
C4' H4' U5P sing 473 n n 
O3' HO3' U5P sing 474 n n 
C5' O5' U5P sing 475 n n 
C5' "H5'1" U5P sing 476 n n 
C5' "H5'2" U5P sing 477 n n 
O5' P U5P sing 478 n n 
P O1P U5P doub 479 n n 
P O2P U5P sing 480 n n 
P O3P U5P sing 481 n n 
O2P HOP2 U5P sing 482 n n 
O3P HOP3 U5P sing 483 n n 
#
_atom_sites.entry_id                     3GF4 
_atom_sites.fract_transf_matrix[1][1]    0.010644 
_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]    0.010644 
_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]    0.007677 
_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 FAD A 1 391 391 FAD FAD . 
D 3 UPG A 1 392 392 UPG UPG . 
E 2 FAD B 1 391 391 FAD FAD . 
F 4 U5P B 1 392 392 U5P U5P . 
G 5 HOH A 1 393 393 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 5 397 397 HOH HOH . 
G 5 HOH A 6 398 398 HOH HOH . 
G 5 HOH A 7 401 401 HOH HOH . 
G 5 HOH A 8 402 402 HOH HOH . 
G 5 HOH A 9 405 405 HOH HOH . 
G 5 HOH A 10 409 409 HOH HOH . 
G 5 HOH A 11 416 416 HOH HOH . 
G 5 HOH A 12 417 417 HOH HOH . 
G 5 HOH A 13 418 418 HOH HOH . 
G 5 HOH A 14 421 421 HOH HOH . 
G 5 HOH A 15 422 422 HOH HOH . 
G 5 HOH A 16 427 427 HOH HOH . 
G 5 HOH A 17 428 428 HOH HOH . 
G 5 HOH A 18 429 429 HOH HOH . 
G 5 HOH A 19 430 430 HOH HOH . 
G 5 HOH A 20 431 431 HOH HOH . 
G 5 HOH A 21 433 433 HOH HOH . 
G 5 HOH A 22 436 436 HOH HOH . 
G 5 HOH A 23 437 437 HOH HOH . 
G 5 HOH A 24 440 440 HOH HOH . 
G 5 HOH A 25 441 441 HOH HOH . 
G 5 HOH A 26 442 442 HOH HOH . 
G 5 HOH A 27 447 447 HOH HOH . 
G 5 HOH A 28 448 448 HOH HOH . 
G 5 HOH A 29 449 449 HOH HOH . 
G 5 HOH A 30 450 450 HOH HOH . 
G 5 HOH A 31 452 452 HOH HOH . 
G 5 HOH A 32 454 454 HOH HOH . 
G 5 HOH A 33 458 458 HOH HOH . 
G 5 HOH A 34 463 463 HOH HOH . 
G 5 HOH A 35 465 465 HOH HOH . 
G 5 HOH A 36 467 467 HOH HOH . 
G 5 HOH A 37 470 470 HOH HOH . 
G 5 HOH A 38 472 472 HOH HOH . 
G 5 HOH A 39 475 475 HOH HOH . 
G 5 HOH A 40 476 476 HOH HOH . 
G 5 HOH A 41 477 477 HOH HOH . 
G 5 HOH A 42 478 478 HOH HOH . 
G 5 HOH A 43 479 479 HOH HOH . 
G 5 HOH A 44 480 480 HOH HOH . 
G 5 HOH A 45 485 485 HOH HOH . 
G 5 HOH A 46 491 491 HOH HOH . 
G 5 HOH A 47 492 492 HOH HOH . 
G 5 HOH A 48 493 493 HOH HOH . 
G 5 HOH A 49 495 495 HOH HOH . 
G 5 HOH A 50 496 496 HOH HOH . 
G 5 HOH A 51 497 497 HOH HOH . 
G 5 HOH A 52 498 498 HOH HOH . 
G 5 HOH A 53 499 499 HOH HOH . 
G 5 HOH A 54 500 500 HOH HOH . 
G 5 HOH A 55 501 501 HOH HOH . 
G 5 HOH A 56 502 502 HOH HOH . 
G 5 HOH A 57 503 503 HOH HOH . 
G 5 HOH A 58 504 504 HOH HOH . 
G 5 HOH A 59 505 505 HOH HOH . 
G 5 HOH A 60 506 506 HOH HOH . 
G 5 HOH A 61 507 507 HOH HOH . 
G 5 HOH A 62 508 508 HOH HOH . 
G 5 HOH A 63 509 509 HOH HOH . 
G 5 HOH A 64 510 510 HOH HOH . 
G 5 HOH A 65 514 514 HOH HOH . 
G 5 HOH A 66 515 515 HOH HOH . 
G 5 HOH A 67 516 516 HOH HOH . 
G 5 HOH A 68 517 517 HOH HOH . 
G 5 HOH A 69 518 518 HOH HOH . 
G 5 HOH A 70 519 519 HOH HOH . 
G 5 HOH A 71 520 520 HOH HOH . 
G 5 HOH A 72 521 521 HOH HOH . 
G 5 HOH A 73 522 522 HOH HOH . 
G 5 HOH A 74 532 532 HOH HOH . 
G 5 HOH A 75 533 533 HOH HOH . 
G 5 HOH A 76 534 534 HOH HOH . 
G 5 HOH A 77 536 536 HOH HOH . 
G 5 HOH A 78 537 537 HOH HOH . 
G 5 HOH A 79 538 538 HOH HOH . 
G 5 HOH A 80 539 539 HOH HOH . 
G 5 HOH A 81 545 545 HOH HOH . 
G 5 HOH A 82 546 546 HOH HOH . 
G 5 HOH A 83 547 547 HOH HOH . 
G 5 HOH A 84 548 548 HOH HOH . 
G 5 HOH A 85 549 549 HOH HOH . 
G 5 HOH A 86 550 550 HOH HOH . 
G 5 HOH A 87 551 551 HOH HOH . 
G 5 HOH A 88 552 552 HOH HOH . 
G 5 HOH A 89 553 553 HOH HOH . 
G 5 HOH A 90 554 554 HOH HOH . 
G 5 HOH A 91 556 556 HOH HOH . 
G 5 HOH A 92 558 558 HOH HOH . 
G 5 HOH A 93 559 559 HOH HOH . 
G 5 HOH A 94 560 560 HOH HOH . 
G 5 HOH A 95 581 581 HOH HOH . 
G 5 HOH A 96 582 582 HOH HOH . 
G 5 HOH A 97 583 583 HOH HOH . 
H 5 HOH B 1 393 393 HOH HOH . 
H 5 HOH B 2 394 394 HOH HOH . 
H 5 HOH B 3 395 395 HOH HOH . 
H 5 HOH B 4 397 397 HOH HOH . 
H 5 HOH B 5 399 399 HOH HOH . 
H 5 HOH B 6 400 400 HOH HOH . 
H 5 HOH B 7 403 403 HOH HOH . 
H 5 HOH B 8 404 404 HOH HOH . 
H 5 HOH B 9 406 406 HOH HOH . 
H 5 HOH B 10 407 407 HOH HOH . 
H 5 HOH B 11 408 408 HOH HOH . 
H 5 HOH B 12 410 410 HOH HOH . 
H 5 HOH B 13 411 411 HOH HOH . 
H 5 HOH B 14 412 412 HOH HOH . 
H 5 HOH B 15 413 413 HOH HOH . 
H 5 HOH B 16 414 414 HOH HOH . 
H 5 HOH B 17 415 415 HOH HOH . 
H 5 HOH B 18 419 419 HOH HOH . 
H 5 HOH B 19 420 420 HOH HOH . 
H 5 HOH B 20 423 423 HOH HOH . 
H 5 HOH B 21 424 424 HOH HOH . 
H 5 HOH B 22 425 425 HOH HOH . 
H 5 HOH B 23 426 426 HOH HOH . 
H 5 HOH B 24 432 432 HOH HOH . 
H 5 HOH B 25 434 434 HOH HOH . 
H 5 HOH B 26 435 435 HOH HOH . 
H 5 HOH B 27 438 438 HOH HOH . 
H 5 HOH B 28 439 439 HOH HOH . 
H 5 HOH B 29 443 443 HOH HOH . 
H 5 HOH B 30 444 444 HOH HOH . 
H 5 HOH B 31 445 445 HOH HOH . 
H 5 HOH B 32 446 446 HOH HOH . 
H 5 HOH B 33 451 451 HOH HOH . 
H 5 HOH B 34 453 453 HOH HOH . 
H 5 HOH B 35 455 455 HOH HOH . 
H 5 HOH B 36 456 456 HOH HOH . 
H 5 HOH B 37 457 457 HOH HOH . 
H 5 HOH B 38 459 459 HOH HOH . 
H 5 HOH B 39 460 460 HOH HOH . 
H 5 HOH B 40 461 461 HOH HOH . 
H 5 HOH B 41 462 462 HOH HOH . 
H 5 HOH B 42 464 464 HOH HOH . 
H 5 HOH B 43 466 466 HOH HOH . 
H 5 HOH B 44 468 468 HOH HOH . 
H 5 HOH B 45 469 469 HOH HOH . 
H 5 HOH B 46 471 471 HOH HOH . 
H 5 HOH B 47 473 473 HOH HOH . 
H 5 HOH B 48 474 474 HOH HOH . 
H 5 HOH B 49 481 481 HOH HOH . 
H 5 HOH B 50 482 482 HOH HOH . 
H 5 HOH B 51 483 483 HOH HOH . 
H 5 HOH B 52 484 484 HOH HOH . 
H 5 HOH B 53 486 486 HOH HOH . 
H 5 HOH B 54 487 487 HOH HOH . 
H 5 HOH B 55 488 488 HOH HOH . 
H 5 HOH B 56 489 489 HOH HOH . 
H 5 HOH B 57 490 490 HOH HOH . 
H 5 HOH B 58 494 494 HOH HOH . 
H 5 HOH B 59 511 511 HOH HOH . 
H 5 HOH B 60 512 512 HOH HOH . 
H 5 HOH B 61 513 513 HOH HOH . 
H 5 HOH B 62 523 523 HOH HOH . 
H 5 HOH B 63 524 524 HOH HOH . 
H 5 HOH B 64 525 525 HOH HOH . 
H 5 HOH B 65 526 526 HOH HOH . 
H 5 HOH B 66 527 527 HOH HOH . 
H 5 HOH B 67 528 528 HOH HOH . 
H 5 HOH B 68 529 529 HOH HOH . 
H 5 HOH B 69 530 530 HOH HOH . 
H 5 HOH B 70 531 531 HOH HOH . 
H 5 HOH B 71 535 535 HOH HOH . 
H 5 HOH B 72 540 540 HOH HOH . 
H 5 HOH B 73 541 541 HOH HOH . 
H 5 HOH B 74 542 542 HOH HOH . 
H 5 HOH B 75 543 543 HOH HOH . 
H 5 HOH B 76 544 544 HOH HOH . 
H 5 HOH B 77 555 555 HOH HOH . 
H 5 HOH B 78 557 557 HOH HOH . 
H 5 HOH B 79 561 561 HOH HOH . 
H 5 HOH B 80 562 562 HOH HOH . 
H 5 HOH B 81 563 563 HOH HOH . 
H 5 HOH B 82 564 564 HOH HOH . 
H 5 HOH B 83 565 565 HOH HOH . 
H 5 HOH B 84 566 566 HOH HOH . 
H 5 HOH B 85 567 567 HOH HOH . 
H 5 HOH B 86 568 568 HOH HOH . 
H 5 HOH B 87 569 569 HOH HOH . 
H 5 HOH B 88 570 570 HOH HOH . 
H 5 HOH B 89 571 571 HOH HOH . 
H 5 HOH B 90 572 572 HOH HOH . 
H 5 HOH B 91 573 573 HOH HOH . 
H 5 HOH B 92 574 574 HOH HOH . 
H 5 HOH B 93 575 575 HOH HOH . 
H 5 HOH B 94 576 576 HOH HOH . 
H 5 HOH B 95 577 577 HOH HOH . 
H 5 HOH B 96 578 578 HOH HOH . 
H 5 HOH B 97 579 579 HOH HOH . 
H 5 HOH B 98 580 580 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 U5P . . . F 4 7.412 -29.215 -3.952 1 62.79 ? N1 U5P 392 B 1 
HETATM 2 C C2 U5P . . . F 4 6.528 -28.129 -3.602 1 62.75 ? C2 U5P 392 B 1 
HETATM 3 N N3 U5P . . . F 4 5.173 -28.321 -3.641 1 62.89 ? N3 U5P 392 B 1 
HETATM 4 C C4 U5P . . . F 4 4.645 -29.534 -3.999 1 64.21 ? C4 U5P 392 B 1 
HETATM 5 C C5 U5P . . . F 4 5.501 -30.61 -4.352 1 63.99 ? C5 U5P 392 B 1 
HETATM 6 C C6 U5P . . . F 4 6.895 -30.419 -4.321 1 64.92 ? C6 U5P 392 B 1 
HETATM 7 O O2 U5P . . . F 4 7.01 -26.994 -3.263 1 59.85 ? O2 U5P 392 B 1 
HETATM 8 O O4 U5P . . . F 4 3.37 -29.712 -4.02 1 63.26 ? O4 U5P 392 B 1 
HETATM 9 C C1' U5P . . . F 4 8.883 -29.004 -3.942 1 62.15 ? C1' U5P 392 B 1 
HETATM 10 C C2' U5P . . . F 4 9.488 -29.071 -2.53 1 61.06 ? C2' U5P 392 B 1 
HETATM 11 O O2' U5P . . . F 4 10.536 -28.07 -2.468 1 53.93 ? O2' U5P 392 B 1 
HETATM 12 C C3' U5P . . . F 4 10.171 -30.416 -2.494 1 60.55 ? C3' U5P 392 B 1 
HETATM 13 C C4' U5P . . . F 4 10.637 -30.597 -3.968 1 62.14 ? C4' U5P 392 B 1 
HETATM 14 O O3' U5P . . . F 4 11.264 -30.284 -1.571 1 57.07 ? O3' U5P 392 B 1 
HETATM 15 O O4' U5P . . . F 4 9.607 -29.963 -4.766 1 59.95 ? O4' U5P 392 B 1 
HETATM 16 C C5' U5P . . . F 4 10.853 -32.07 -4.412 1 64.11 ? C5' U5P 392 B 1 
HETATM 17 O O5' U5P . . . F 4 9.79 -32.556 -5.295 1 63 ? O5' U5P 392 B 1 
HETATM 18 P P U5P . . . F 4 9.247 -34.136 -5.248 1 63.04 ? P U5P 392 B 1 
HETATM 19 O O1P U5P . . . F 4 9.776 -34.794 -6.575 1 59.33 ? O1P U5P 392 B 1 
HETATM 20 O O2P U5P . . . F 4 9.843 -34.746 -3.936 1 57.44 ? O2P U5P 392 B 1 
HETATM 21 O O3P U5P . . . F 4 7.678 -33.937 -5.239 1 60.33 ? O3P U5P 392 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#