Research workbench
Histone lysine desuccinylase SIRT5 in complex with succinyl peptide H2BK120
Analyse Histone lysine desuccinylase SIRT5 in complex with succinyl peptide H2BK120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ACO
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; Succinyl peptide H2BK120
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- ZN, CL
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 270 | 39% helix, 20% strand | Q9NXA8 |
| B | Succinyl peptide H2BK120 | protein | 7 | 0% helix, 43% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.39 | 0.75 | 26 | empty |
| 2 | 51 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6ACO · histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120 · 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 0.99
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 6ACO · PDBe 6ACO · UniProt Q9NXA8
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