7X3P: Human SIRT5

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9. Determined by X-ray diffraction at 1.56 Å resolution. Released 6 Sept 2023.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,543
Mol. weight: 31.03 kDa
Ligands: ZN, 8VG
Released: 6 Sept 2023

Explore 7X3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7X3P contains 20 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: 20 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
α-helix	72-74	3
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	116-129	14
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
α-helix	214	1
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	257-259	3
α-helix	260-266	7
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	277	Homo sapiens	Q9NXA8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7X3P_1 NAD-dependent protein deacylase sirtuin-5, mitochondrial (chains A)
ARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAH
NPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKN
LLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCG
GLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAE
FNTETTPATNRFRFHFQGPCGTTLPEALACHENETVS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
8VG	5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino…	C31 H33 F3 N6 O6 S	1

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

Primary citation

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9. Li, G.-B., Deng, J. 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
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
8Z55 1.83 Å, Crystal structure of human SIRT5 in complex with succPrx1 and ADP ribose

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