Research workbench
The structure of SIR2AF1 bound to a succinylated histone peptide
Analyse The structure of SIR2AF1 bound to a succinylated histone peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TWI
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase 1; Succinylated H4 peptide (AA8-20)
- EC
- 3.5.1.-
- UniProt
- O28597, P02309
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase 1 (EC 3.5.1.-) | protein | 244 | 40% helix, 19% strand | O28597 |
| B | Succinylated H4 peptide (AA8-20) | protein | 8 | 0% helix, 25% strand | P02309 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.77 | 0.92 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4TWI · The structure of Sir2Af1 bound to a succinylated histone peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O28597 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase 1 (O28597) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain B against A, TM-score 0.31
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 O28597
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 4TWI · PDBe 4TWI · UniProt O28597 · UniProt P02309
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