6LJM: Human Sirt5

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13. Determined by X-ray diffraction at 1.78 Å resolution. Released 28 Oct 2020.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,438
Mol. weight: 30.34 kDa
Ligands: MCM, ZN
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

6LJM 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	145-148	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	229-241	13
β-strand	244-248	5	1
α-helix	257-266	10
β-strand	271-275	5	1
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	272	Homo sapiens	Q9NXA8 (AlphaFold model)
Ace-ser-leu-gly-sll	B	protein	5	synthetic construct

Sequence of entity 1 (A), FASTA

>6LJM_1 NAD-dependent protein deacylase sirtuin-5, mitochondrial (chains A)
QASARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLA
FAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAG
TKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEA
GCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVP
VAEFNTETTPATNRFRFHFQGPCGTTLPEALA

Sequence of entity 2 (B), FASTA

>6LJM_2 ACE-SER-LEU-GLY-SLL (chains B)
XSLGX

Ligands and cofactors

ID	Name	Formula	Copies
MCM	7-amino-4-methyl-chromen-2-one	C10 H9 N O2	1
ZN	Zinc ion	Zn	1

Primary citation

Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery. Yang, L.L., Wang, H.L., Yan, Y.H. et al. Eur J Med Chem (2020) 192:112201-112201. DOI 10.1016/j.ejmech.2020.112201 · 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
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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