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Human SIRT5 bound to succ-IDH2 and carba-NAD

Analyse Human SIRT5 bound to succ-IDH2 and carba-NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G1C
Type: protein
Length: 544 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial; Succinylated IDH2 peptide
EC: 3.5.1.-
UniProt: Q9NXA8
Ligands: ACE, CNA, ZN, NH2
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-)	protein	267	39% helix, 20% strand	Q9NXA8
D, E	Succinylated IDH2 peptide	protein	5	0% helix, 40% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, D, B, E
CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · chains A, D
ZN · Zinc ion · metal · 2 copies · chains A, B
NH2 · Amino group · ion · 2 copies · chains A, B, D, E

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	352	0.80	0.90	56	CNA
2	346	0.74	0.85	53	empty
3	56	0.69	0.96	19	empty
4	77	0.32	0.74	20	empty
5	65	0.31	0.75	19	empty

Interfaces

6 interfaces between chains.

A–B · 1158 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 523 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 510 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 135 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 103 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified, 1 disulfide (covalent ligand, nonstandard, disulfide).

Compared structures

4G1C · Human SIRT5 bound to Succ-IDH2 and Carba-NAD · the same entry in another collection · chain A against A, 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 A against A, TM-score 1.00

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 4G1C · PDBe 4G1C · UniProt Q9NXA8

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