2NYR: Human Sirtuin Homolog 5

Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin. Determined by X-ray diffraction at 2.06 Å resolution. Released 19 Dec 2006.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,288
Mol. weight: 60.28 kDa
Ligands: ZN, SVR
Released: 19 Dec 2006

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

Secondary structure: helices and β-sheets

2NYR contains 37 α-helices and 28 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, 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	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	116-129	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	261-265	5
β-strand	271-275	5	1
β-strand	287-290	4	1
α-helix	293-300	8

Chain B: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	5
α-helix	40-47	8
β-strand	52-57	6	5
α-helix	59-63	5
α-helix	67-69	3
β-strand	77	1	6
β-strand	80	1	6
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	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	260-265	6
β-strand	271-275	5	5
β-strand	287-290	4	5
α-helix	293-300	8

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>2NYR_1 NAD-dependent deacetylase sirtuin-5 (chains A, B)
GSARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAF
AHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGT
KNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAG
CGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPV
AEFNTETTPATNRFRFHFQGPCGTTLPEALA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
SVR	8,8'-[carbonylbis[imino-3,1-PHENYLENECARBONYLIMINO(4-methyl-3,1-phenylene)carbo…	C51 H40 N6 O23 S6	1

Primary citation

Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin. Schuetz, A., Min, J., Antoshenko, T. et al. Structure (2007) 15:377-389. DOI 10.1016/j.str.2007.02.002 · 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
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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