data_3GF4 # _model_server_result.job_id A3oS0b6PxQcbkzoApIA4YQ _model_server_result.datetime_utc '2024-11-24 17:30:12' _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":"D","auth_seq_id":392}' # _entry.id 3GF4 # _exptl.entry_id 3GF4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 UPG sing 484 n n N1 C6 UPG sing 485 n n N1 C1C UPG sing 486 n n C2 N3 UPG sing 487 n n C2 O2 UPG doub 488 n n N3 C4 UPG sing 489 n n N3 HN3 UPG sing 490 n n C4 C5 UPG sing 491 n n C4 O4 UPG doub 492 n n C5 C6 UPG doub 493 n n C5 H5 UPG sing 494 n n C6 H6 UPG sing 495 n n C1C C2C UPG sing 496 n n C1C O4C UPG sing 497 n n C1C H1C UPG sing 498 n n C2C O2C UPG sing 499 n n C2C C3C UPG sing 500 n n C2C H2C UPG sing 501 n n O2C HO2C UPG sing 502 n n C3C C4C UPG sing 503 n n C3C O3C UPG sing 504 n n C3C H3C UPG sing 505 n n C4C O4C UPG sing 506 n n C4C C5C UPG sing 507 n n C4C H4C UPG sing 508 n n O3C HO3C UPG sing 509 n n C5C O5C UPG sing 510 n n C5C H5C1 UPG sing 511 n n C5C H5C2 UPG sing 512 n n O5C PA UPG sing 513 n n PA O1A UPG doub 514 n n PA O2A UPG sing 515 n n PA O3A UPG sing 516 n n O2A HOA2 UPG sing 517 n n O3A PB UPG sing 518 n n PB O1B UPG doub 519 n n PB O2B UPG sing 520 n n PB O3B UPG sing 521 n n O2B HOB2 UPG sing 522 n n O3B C1' UPG sing 523 n n C1' C2' UPG sing 524 n n C1' O5' UPG sing 525 n n C1' H1' UPG sing 526 n n C2' C3' UPG sing 527 n n C2' O2' UPG sing 528 n n C2' H2' UPG sing 529 n n C3' C4' UPG sing 530 n n C3' O3' UPG sing 531 n n C3' H3' UPG sing 532 n n C4' C5' UPG sing 533 n n C4' O4' UPG sing 534 n n C4' H4' UPG sing 535 n n C5' C6' UPG sing 536 n n C5' O5' UPG sing 537 n n C5' H5' UPG sing 538 n n C6' O6' UPG sing 539 n n C6' "H6'1" UPG sing 540 n n C6' "H6'2" UPG sing 541 n n O2' HO2' UPG sing 542 n n O3' HO3' UPG sing 543 n n O4' HO4' UPG sing 544 n n O6' HO6' UPG sing 545 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 UPG . . . D 3 -27.976 -37.754 -0.415 1 44.21 ? N1 UPG 392 A 1 HETATM 2 C C2 UPG . . . D 3 -28.029 -36.529 -1.132 1 42.33 ? C2 UPG 392 A 1 HETATM 3 N N3 UPG . . . D 3 -27.018 -36.128 -1.912 1 41.38 ? N3 UPG 392 A 1 HETATM 4 C C4 UPG . . . D 3 -25.944 -36.897 -2.024 1 40.06 ? C4 UPG 392 A 1 HETATM 5 C C5 UPG . . . D 3 -25.827 -38.125 -1.365 1 38.95 ? C5 UPG 392 A 1 HETATM 6 C C6 UPG . . . D 3 -26.892 -38.571 -0.571 1 40.64 ? C6 UPG 392 A 1 HETATM 7 O O2 UPG . . . D 3 -29.021 -35.813 -1.035 1 43.55 ? O2 UPG 392 A 1 HETATM 8 O O4 UPG . . . D 3 -25.066 -36.462 -2.756 1 43.33 ? O4 UPG 392 A 1 HETATM 9 C C1C UPG . . . D 3 -29.16 -38.092 0.385 1 43.74 ? C1C UPG 392 A 1 HETATM 10 C C2C UPG . . . D 3 -30.105 -38.835 -0.551 1 45.33 ? C2C UPG 392 A 1 HETATM 11 O O2C UPG . . . D 3 -31.463 -38.415 -0.342 1 44.08 ? O2C UPG 392 A 1 HETATM 12 C C3C UPG . . . D 3 -29.812 -40.283 -0.178 1 44.53 ? C3C UPG 392 A 1 HETATM 13 C C4C UPG . . . D 3 -29.52 -40.223 1.314 1 45.03 ? C4C UPG 392 A 1 HETATM 14 O O4C UPG . . . D 3 -28.878 -38.952 1.493 1 43.8 ? O4C UPG 392 A 1 HETATM 15 O O3C UPG . . . D 3 -30.846 -41.181 -0.533 1 46.38 ? O3C UPG 392 A 1 HETATM 16 C C5C UPG . . . D 3 -28.621 -41.349 1.836 1 48.88 ? C5C UPG 392 A 1 HETATM 17 O O5C UPG . . . D 3 -27.4 -41.338 1.099 1 54.7 ? O5C UPG 392 A 1 HETATM 18 P PA UPG . . . D 3 -26.364 -42.545 0.989 1 58.82 ? PA UPG 392 A 1 HETATM 19 O O1A UPG . . . D 3 -25.475 -42.293 -0.198 1 60.03 ? O1A UPG 392 A 1 HETATM 20 O O2A UPG . . . D 3 -25.613 -42.739 2.289 1 63.26 ? O2A UPG 392 A 1 HETATM 21 O O3A UPG . . . D 3 -27.206 -43.879 0.799 1 68.66 ? O3A UPG 392 A 1 HETATM 22 P PB UPG . . . D 3 -27.743 -44.131 -0.69 1 76.65 ? PB UPG 392 A 1 HETATM 23 O O1B UPG . . . D 3 -29.229 -44.434 -0.58 1 77.88 ? O1B UPG 392 A 1 HETATM 24 O O2B UPG . . . D 3 -27.462 -43 -1.685 1 74.65 ? O2B UPG 392 A 1 HETATM 25 O O3B UPG . . . D 3 -26.847 -45.405 -1.132 1 78.91 ? O3B UPG 392 A 1 HETATM 26 C C1' UPG . . . D 3 -25.934 -45.358 -2.269 1 78.95 ? C1' UPG 392 A 1 HETATM 27 C C2' UPG . . . D 3 -25.532 -46.788 -2.614 1 79.68 ? C2' UPG 392 A 1 HETATM 28 C C3' UPG . . . D 3 -24.516 -47.351 -1.576 1 79.33 ? C3' UPG 392 A 1 HETATM 29 C C4' UPG . . . D 3 -23.328 -46.386 -1.377 1 77.96 ? C4' UPG 392 A 1 HETATM 30 C C5' UPG . . . D 3 -23.814 -44.948 -1.101 1 74.08 ? C5' UPG 392 A 1 HETATM 31 C C6' UPG . . . D 3 -22.639 -43.967 -1.095 1 71.85 ? C6' UPG 392 A 1 HETATM 32 O O2' UPG . . . D 3 -26.709 -47.625 -2.636 1 80.8 ? O2' UPG 392 A 1 HETATM 33 O O3' UPG . . . D 3 -24.024 -48.623 -2.029 1 78.18 ? O3' UPG 392 A 1 HETATM 34 O O4' UPG . . . D 3 -22.527 -46.838 -0.275 1 78.11 ? O4' UPG 392 A 1 HETATM 35 O O5' UPG . . . D 3 -24.757 -44.557 -2.11 1 75.93 ? O5' UPG 392 A 1 HETATM 36 O O6' UPG . . . D 3 -21.601 -44.325 -2.051 1 64.49 ? O6' UPG 392 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #