6EQS: Human Sirt5

Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29. Determined by X-ray diffraction at 1.32 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 1.32 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,389
Mol. weight: 126.44 kDa
Ligands: ZN, BV8, BU2
Released: 1 Nov 2017

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

Secondary structure: helices and β-sheets

6EQS contains 80 α-helices and 56 β-strands across 4 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: 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	60-63	4
α-helix	67-69	3
α-helix	72-75	4
β-strand	76-77	2	2
β-strand	80-81	2	2
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
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	257-259	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

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	5
α-helix	40-49	10
β-strand	52-57	6	5
α-helix	59-65	7
α-helix	67-69	3
α-helix	72-75	4
β-strand	76-77	2	6
β-strand	80-81	2	6
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
α-helix	116-130	15
β-strand	134-139	6	5
α-helix	145-148	4
β-strand	154-156	3	5
β-strand	159-166	8	7
β-strand	172-174	3	7
α-helix	182-184	3
α-helix	194-196	3
α-helix	201-203	3
β-strand	206	1	8
α-helix	214	1
β-strand	215	1	8
β-strand	216-220	5	7
α-helix	221-222	2
α-helix	226-228	3
α-helix	229-241	13
β-strand	244-248	5	5
α-helix	257-259	3
α-helix	260-266	7
β-strand	271-275	5	5
α-helix	282-284	3
β-strand	287-290	4	5
α-helix	293-300	8

Chain C: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37	1	9
α-helix	40-49	10
β-strand	52-57	6	9
α-helix	59-61	3
α-helix	63-65	3
α-helix	72-75	4
β-strand	76-77	2	10
β-strand	80-81	2	10
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
α-helix	116-129	14
β-strand	134-139	6	9
α-helix	145-148	4
β-strand	154-156	3	9
β-strand	159-166	8	11
β-strand	172-174	3	11
α-helix	182-184	3
α-helix	194-196	3
α-helix	201-203	3
β-strand	206	1	12
α-helix	214	1
β-strand	215	1	12
β-strand	216-220	5	11
α-helix	221-222	2
α-helix	226-228	3
α-helix	229-241	13
β-strand	244-248	5	9
α-helix	257-259	3
α-helix	260-266	7
β-strand	271-275	5	9
α-helix	282-284	3
β-strand	287-290	4	9
α-helix	293-300	8

Chain D: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37	1	13
α-helix	40-49	10
β-strand	52-57	6	13
α-helix	60-63	4
α-helix	72-75	4
β-strand	76-77	2	14
β-strand	80-81	2	14
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
α-helix	116-130	15
β-strand	134-139	6	13
α-helix	145-148	4
β-strand	154-156	3	13
β-strand	159-166	8	15
β-strand	172-174	3	15
α-helix	182-184	3
α-helix	194-196	3
α-helix	201-203	3
β-strand	206	1	16
α-helix	214	1
β-strand	215	1	16
β-strand	216-220	5	15
α-helix	226-228	3
α-helix	229-241	13
β-strand	244-248	5	13
α-helix	257-259	3
α-helix	260-266	7
β-strand	271-275	5	13
α-helix	282-284	3
β-strand	287-290	4	13
α-helix	293-300	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A, B, C, D	protein	275	Homo sapiens	Q9NXA8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6EQS_1 NAD-dependent protein deacylase sirtuin-5, mitochondrial (chains A, B, C, D)
GIDPFTARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLAT
PLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHR
KAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRC
EEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAAR
GVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
BV8	3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6…	C47 H63 N11 O19 P2 S	4
BU2	1,3-butanediol	C4 H10 O2	8

Water and common crystallization additives (EDO, DMS) are not listed.

Primary citation

Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Rajabi, N., Auth, M., Troelsen, K.R. et al. Angew Chem Int Ed Engl (2017) 56:14836-14841. DOI 10.1002/anie.201709050 · PubMed

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

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
8Z55 1.83 Å, Crystal structure of human SIRT5 in complex with succPrx1 and ADP ribose

Browse structure collections

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