8Z55: Human SIRT5

Crystal structure of human SIRT5 in complex with succPrx1 and ADP ribose. Determined by X-ray diffraction at 1.83 Å resolution. Released 9 Oct 2024.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,232
Mol. weight: 31.75 kDa
Ligands: ZN, ADP
Released: 9 Oct 2024

Explore 8Z55 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Z55 contains 17 α-helices and 14 β-strands across 1 chain. 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	1
α-helix	40-49	10
β-strand	52-57	6	1
α-helix	59-63	5
β-strand	77	1	2
β-strand	80	1	2
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-108	14
α-helix	109-111	3
α-helix	116-130	15
β-strand	134-139	6	1
α-helix	145-149	5
β-strand	154-156	3	1
β-strand	159-166	8	3
β-strand	172-174	3	3
α-helix	182-184	3
α-helix	194-196	3
α-helix	201-203	3
β-strand	206	1	4
β-strand	215	1	4
β-strand	216-220	5	3
α-helix	221-222	2
α-helix	225-228	4
α-helix	229-241	13
β-strand	244-248	5	1
α-helix	261-266	6
β-strand	271-275	5	1
α-helix	282-284	3
β-strand	287-290	4	1
α-helix	293-300	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	protein	274	Homo sapiens	Q9NXA8 (AlphaFold model)
Peroxiredoxin-1 fragment	B	protein	9	Homo sapiens	Q06830 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Z55_1 NAD-dependent protein deacylase sirtuin-5, mitochondrial (chains A)
MHHHHHHPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATP
LAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRK
AGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCE
EAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARG
VPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA

Sequence of entity 2 (B), FASTA

>8Z55_2 Peroxiredoxin-1 fragment (chains B)
SKEYFSXQK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD + -binding pocket. Yokoyama, T., Takayama, Y., Mizuguchi, M. et al. FEBS Lett (2024) 598:2269-2280. DOI 10.1002/1873-3468.14961 · PubMed

Other PDB entries of the same protein (UniProt Q9NXA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6EQS 1.32 Å, Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29
6LJK 1.39 Å, Crystal structure of human Sirt5 in complex with an internally quenched fluorescent…
8Z54 1.45 Å, Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment
5BWL 1.55 Å, Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide
3RIY 1.55 Å, Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase
7X3P 1.56 Å, Crystal structure of human SIRT5 in complex with diazirine inhibitor 9
9V0H 1.67 Å, Crystal structure of human SIRT5 in complex with inhibitor 0904
4F56 1.7 Å, The bicyclic intermediate structure provides insights into the desuccinylation mechanism…
6ACO 1.71 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120
6LJM 1.78 Å, Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate…
6LJN 1.8 Å, Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate…
8Z56 1.81 Å, Crystal structure of human Q140L-SIRT5 in complex with succinylated Prx1 fragment

Browse structure collections

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