2B4Y: Human Sirtuin homolog 5

Crystal Structure of Human Sirtuin homolog 5. Determined by X-ray diffraction at 1.9 Å resolution. Released 28 Feb 2006.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,930
Mol. weight: 121.72 kDa
Ligands: ZN, APR
Released: 28 Feb 2006

Explore 2B4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B4Y contains 70 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: 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	59-65	7
β-strand	77	1	2
β-strand	80	1	2
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-110	16
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	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

Chain B: 18 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
β-strand	77	1	6
β-strand	80	1	6
α-helix	82-84	3
α-helix	88-93	6
α-helix	95-110	16
α-helix	116-129	14
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	225-228	4
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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	9
α-helix	40-49	10
β-strand	52-57	6	9
α-helix	59-65	7
β-strand	77	1	10
β-strand	80	1	10
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	9
α-helix	145-149	5
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	229-241	13
β-strand	244-248	5	9
α-helix	257-259	3
α-helix	260-265	6
β-strand	271-275	5	9
α-helix	282-284	3
β-strand	287-290	4	9
α-helix	293-301	9

Chain D: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	13
α-helix	40-49	10
β-strand	52-57	6	13
α-helix	59-61	3
α-helix	63-65	3
β-strand	77	1	14
β-strand	80	1	14
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
α-helix	116-126	11
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	221-222	2
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	293-301	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent deacetylase sirtuin-5	A, B, C, D	protein	271	Homo sapiens	Q9NXA8 (AlphaFold model)

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

>2B4Y_1 NAD-dependent deacetylase sirtuin-5 (chains A, B, C, D)
GSARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAF
AHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGT
KNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAG
CGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPV
AEFNTETTPATNRFRFHFQGPCGTTLPEALA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	4

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

Primary citation

Crystal Structure of Human Sirtuin homolog 5 in complex with NAD. Antoshenko, T., Min, J.R., Schuetz, A. 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

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