6ACE: Histone lysine desuccinylase Sirt5

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122. Determined by X-ray diffraction at 1.98 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,255
Mol. weight: 30.35 kDa
Ligands: ZN
Released: 24 Jul 2019

Explore 6ACE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ACE contains 19 α-helices and 16 β-strands across 2 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: 18 helices, 15 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	145-148	4
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
α-helix	214	1
β-strand	215	1	4
β-strand	216-220	5	3
α-helix	221-222	2
α-helix	226-228	3
α-helix	229-240	12
β-strand	244-248	5	1
β-strand	254-255	2	5
α-helix	257-266	10
β-strand	271-274	4	1
α-helix	282-284	3
β-strand	287-289	3	1
α-helix	293-300	8

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	119-121	3
β-strand	123-124	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	protein	267	Homo sapiens	Q9NXA8 (AlphaFold model)
succinyl peptide H3K122	B	protein	8	Homo sapiens	Q71DI3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ACE_1 NAD-dependent protein deacylase sirtuin-5, mitochondrial (chains A)
PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNP
SRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLL
EIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGL
LRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFN
TETTPATNRFRFHFQGPCGTTLPEALA

Sequence of entity 2 (B), FASTA

>6ACE_2 succinyl peptide H3K122 (chains B)
TIMPXDIQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122. Hang, T.R., Chen, W.B., Zang, J.Y. et al. To be published.

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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