MolNFT v1 · #31749 · protein

Crystal structure of human sirtuin homolog 5

2B4Y · NAD-dependent deacetylase sirtuin-5: “Crystal structure of human sirtuin homolog 5”. X-ray diffraction, 2 ligands (APR, ZN), 14 pockets (best druggability 0.75). MolNFT v1 #31749 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2B4Y
Type: protein
Length: 1,047 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent deacetylase sirtuin-5
EC: 3.5.1.-
UniProt: Q9NXA8
Ligands: APR, ZN
Pockets: 14 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-)	protein	260	39% helix, 19% strand	Q9NXA8
B	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-)	protein	262	38% helix, 19% strand	Q9NXA8
C	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-)	protein	263	39% helix, 19% strand	Q9NXA8
D	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-)	protein	262	37% helix, 19% strand	Q9NXA8

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.75	0.78	89	empty
2	497	0.71	0.81	54	APR, EPE
3	475	0.69	0.80	57	APR, EPE
4	500	0.64	0.76	42	APR, EPE
5	205	0.60	0.81	35	empty

Interfaces

4 interfaces between chains.

A–B · 532 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 426 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 199 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 46 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2B4Y · Crystal Structure of Human Sirtuin homolog 5 · the same entry in another collection · chain D against D, TM-score 1.00
Q9NXA8 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain D against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9NXA8
Elsewhere: RCSB PDB 2B4Y · PDBe 2B4Y · UniProt Q9NXA8

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