7NKU: Diazaborine bound Drg1(AFG2)
diazaborine bound Drg1(AFG2). Determined by electron microscopy at 3.4 Å resolution. Released 23 Jun 2021.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 6
- Atoms
- 25,332
- Mol. weight
- 517.02 kDa
- Ligands
- TDB, AGS
- Released
- 23 Jun 2021
Explore 7NKU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7NKU contains 197 α-helices and 91 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 31 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 251-262 | 12 | |
| α-helix | 269-274 | 6 | |
| β-strand | 282-284 | 3 | 1 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 1 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 1 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 1 |
| β-strand | 407-409 | 3 | 1 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 2 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| β-strand | 486 | 1 | 2 |
| α-helix | 488-498 | 11 | |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 534-536 | 3 | |
| α-helix | 539-544 | 6 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 3 |
| α-helix | 564-572 | 9 | |
| β-strand | 577-582 | 6 | 3 |
| α-helix | 584-587 | 4 | |
| α-helix | 593-607 | 15 | |
| β-strand | 611-616 | 6 | 3 |
| α-helix | 618-620 | 3 | |
| α-helix | 628-644 | 17 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 3 |
| α-helix | 662-664 | 3 | |
| α-helix | 667-669 | 3 | |
| β-strand | 675-680 | 6 | 3 |
| α-helix | 684-685 | 2 | |
| α-helix | 686-696 | 11 | |
| α-helix | 703-705 | 3 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-756 | 10 | |
| α-helix | 763-775 | 13 | |
| β-strand | 778 | 1 | 3 |
Chain B: 34 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 240-242 | 3 | |
| α-helix | 251-262 | 12 | |
| α-helix | 269-272 | 4 | |
| α-helix | 277-278 | 2 | |
| β-strand | 282-284 | 3 | 4 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 4 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 4 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 4 |
| β-strand | 407-409 | 3 | 4 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 5 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| β-strand | 486 | 1 | 5 |
| α-helix | 488-498 | 11 | |
| α-helix | 506 | 1 | |
| β-strand | 508 | 1 | 6 |
| α-helix | 509-510 | 2 | |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 534-537 | 4 | |
| α-helix | 539-545 | 7 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 6 |
| β-strand | 559 | 1 | 7 |
| β-strand | 561 | 1 | 7 |
| α-helix | 564-572 | 9 | |
| β-strand | 577 | 1 | 6 |
| β-strand | 580-582 | 3 | 6 |
| α-helix | 584-587 | 4 | |
| α-helix | 591-607 | 17 | |
| β-strand | 611-616 | 6 | 6 |
| α-helix | 618-620 | 3 | |
| α-helix | 629-644 | 16 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 6 |
| α-helix | 662-664 | 3 | |
| α-helix | 667-669 | 3 | |
| β-strand | 675-680 | 6 | 6 |
| α-helix | 686-696 | 11 | |
| α-helix | 703-705 | 3 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-755 | 9 | |
| β-strand | 757 | 1 | 8 |
| α-helix | 763-775 | 13 | |
| β-strand | 778 | 1 | 6 |
Chain C: 33 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 240-242 | 3 | |
| α-helix | 251-262 | 12 | |
| α-helix | 269-272 | 4 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281-284 | 4 | 9 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 9 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 9 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 9 |
| β-strand | 405-409 | 5 | 9 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 10 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| β-strand | 486 | 1 | 10 |
| α-helix | 488-498 | 11 | |
| α-helix | 506 | 1 | |
| β-strand | 508 | 1 | 8 |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 539-545 | 7 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 8 |
| α-helix | 564-572 | 9 | |
| β-strand | 577-582 | 6 | 8 |
| α-helix | 583-585 | 3 | |
| α-helix | 591-607 | 17 | |
| β-strand | 611-616 | 6 | 8 |
| α-helix | 618-620 | 3 | |
| α-helix | 629-644 | 16 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 8 |
| α-helix | 662-664 | 3 | |
| α-helix | 667-669 | 3 | |
| β-strand | 675-680 | 6 | 8 |
| α-helix | 686-696 | 11 | |
| α-helix | 703-705 | 3 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-756 | 10 | |
| α-helix | 757-759 | 3 | |
| α-helix | 763-775 | 13 | |
| β-strand | 778 | 1 | 8 |
Chain D: 35 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 240-242 | 3 | |
| α-helix | 251-262 | 12 | |
| α-helix | 268-272 | 5 | |
| α-helix | 277-278 | 2 | |
| β-strand | 282-284 | 3 | 11 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 11 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 11 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 11 |
| β-strand | 407-409 | 3 | 11 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 12 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| α-helix | 484-485 | 2 | |
| β-strand | 486 | 1 | 12 |
| α-helix | 488-498 | 11 | |
| α-helix | 506 | 1 | |
| β-strand | 508 | 1 | 13 |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 534-537 | 4 | |
| α-helix | 539-545 | 7 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 13 |
| α-helix | 564-572 | 9 | |
| β-strand | 577-581 | 5 | 13 |
| α-helix | 583-586 | 4 | |
| α-helix | 591-607 | 17 | |
| β-strand | 611-616 | 6 | 13 |
| α-helix | 618-620 | 3 | |
| α-helix | 627-630 | 4 | |
| α-helix | 633-644 | 12 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 13 |
| α-helix | 662-664 | 3 | |
| α-helix | 667-669 | 3 | |
| β-strand | 675-680 | 6 | 13 |
| α-helix | 686-696 | 11 | |
| α-helix | 703-705 | 3 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-756 | 10 | |
| α-helix | 763-774 | 12 | |
| β-strand | 778 | 1 | 13 |
Chain E: 34 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 240-242 | 3 | |
| α-helix | 251-262 | 12 | |
| α-helix | 268-273 | 6 | |
| α-helix | 276-278 | 3 | |
| β-strand | 282-284 | 3 | 14 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 14 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 14 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 14 |
| β-strand | 407-409 | 3 | 14 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 15 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| α-helix | 484-485 | 2 | |
| β-strand | 486 | 1 | 15 |
| α-helix | 488-498 | 11 | |
| α-helix | 506 | 1 | |
| β-strand | 508 | 1 | 16 |
| α-helix | 509-510 | 2 | |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 534-537 | 4 | |
| α-helix | 539-545 | 7 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 16 |
| β-strand | 559 | 1 | 17 |
| β-strand | 561 | 1 | 17 |
| α-helix | 564-572 | 9 | |
| β-strand | 577 | 1 | 16 |
| β-strand | 580-582 | 3 | 16 |
| α-helix | 583-586 | 4 | |
| α-helix | 591-607 | 17 | |
| β-strand | 611-616 | 6 | 16 |
| α-helix | 618-620 | 3 | |
| α-helix | 628-645 | 18 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 16 |
| α-helix | 662-664 | 3 | |
| α-helix | 667-669 | 3 | |
| β-strand | 677-680 | 4 | 16 |
| α-helix | 686-696 | 11 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-755 | 9 | |
| β-strand | 757 | 1 | 18 |
| α-helix | 763-775 | 13 | |
| β-strand | 778 | 1 | 16 |
Chain F: 30 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 240-242 | 3 | |
| α-helix | 251-262 | 12 | |
| α-helix | 269-272 | 4 | |
| β-strand | 282-284 | 3 | 19 |
| α-helix | 292-302 | 11 | |
| β-strand | 306-310 | 5 | 19 |
| α-helix | 312-314 | 3 | |
| α-helix | 320-336 | 17 | |
| β-strand | 340-345 | 6 | 19 |
| α-helix | 347-349 | 3 | |
| α-helix | 363-374 | 12 | |
| β-strand | 383-388 | 6 | 19 |
| β-strand | 407-409 | 3 | 19 |
| α-helix | 416-429 | 14 | |
| β-strand | 435 | 1 | 20 |
| α-helix | 439-447 | 9 | |
| α-helix | 455-475 | 21 | |
| β-strand | 486 | 1 | 20 |
| α-helix | 488-498 | 11 | |
| α-helix | 506 | 1 | |
| β-strand | 508 | 1 | 18 |
| α-helix | 522-528 | 7 | |
| α-helix | 529-533 | 5 | |
| α-helix | 539-544 | 6 | |
| α-helix | 548-550 | 3 | |
| β-strand | 552-556 | 5 | 18 |
| α-helix | 564-572 | 9 | |
| β-strand | 577-582 | 6 | 18 |
| α-helix | 583-585 | 3 | |
| α-helix | 591-607 | 17 | |
| β-strand | 611-616 | 6 | 18 |
| α-helix | 618-620 | 3 | |
| α-helix | 627-645 | 19 | |
| α-helix | 647-649 | 3 | |
| β-strand | 653-659 | 7 | 18 |
| α-helix | 662-664 | 3 | |
| β-strand | 677-680 | 4 | 18 |
| α-helix | 686-696 | 11 | |
| α-helix | 703-705 | 3 | |
| α-helix | 709-715 | 7 | |
| α-helix | 721-738 | 18 | |
| α-helix | 747-756 | 10 | |
| α-helix | 763-775 | 13 | |
| β-strand | 778 | 1 | 18 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| ATPase family gene 2 protein | A, B, C, D, E, F | protein | 780 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32794 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>7NKU_1 ATPase family gene 2 protein (chains A, B, C, D, E, F)
MAPKSSSSGSKKKSSASSNSADAKASKFKLPAEFITRPHPSKDHGKETCTAYIHPNVLSS
LEINPGSFCTVGKIGENGILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQ
VQPPYATKVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDVVI
TDASDDSLPDVSQLDLNMDDMYGGLDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPE
PLSYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLRVVA
NTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDEIDSIAPNRANDDSG
EVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDPALRRPGRFDQEVEIGIPDVDARF
DILTKQFSRMSSDRHVLDSEAIKYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANID
KFSLKVTLKDVESAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASE
TFARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERAIRE
IFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDGVEELKGVVIVAATN
RPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCTKKFNTEESGVDLHELADRTEGYS
GAEVVLLCQEAGLAAIMEDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRSGSSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| TDB | 6-methyl-2(PROPANE-1-sulfonyl)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-ol | C9 H13 B N2 O3 S2 | 6 |
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 12 |
Primary citation
Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Prattes, M., Grishkovskaya, I., Hodirnau, V.V. et al. Nat Commun (2021) 12:3483-3483. DOI 10.1038/s41467-021-23854-x · PubMed
Other PDB entries of the same protein (UniProt P32794 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7Z11 3.2 Å, Structure of substrate bound DRG1 (AFG2)
- 7WBB 3.6 Å, Cryo-EM structure of substrate engaged Drg1 hexamer
- 7WD3 3.8 Å, Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine
- 7Z34 3.8 Å, Structure of pre-60S particle bound to DRG1(AFG2).
- 7YKZ 4.3 Å, Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine
- 7YKL 5.6 Å, Cryo-EM structure of Drg1 hexamer treated with AMPPNP
- 7YKK 5.9 Å, Cryo-EM structure of Drg1 hexamer treated with ADP
- 7YKT 5.9 Å, Cryo-EM structure of Drg1 hexamer in helical state treated with…
Browse structure collections
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