MolNFT v1 · #106994 · protein
The structure of SIR2AF2 bound to a myristoylated histone peptide
4TWJ · NAD-dependent protein deacylase 2: “The structure of SIR2AF2 bound to a myristoylated histone peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.53). MolNFT v1 #106994 on GenesisL1: 3D structure, binding…
- PDB
- 4TWJ
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase 2; Histone H4 peptide
- EC
- 3.5.1.-
- UniProt
- O30124, P02309
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase 2 (EC 3.5.1.-) | protein | 236 | 43% helix, 22% strand | O30124 |
| B | Histone H4 peptide | protein | 10 | 0% helix, 30% strand | P02309 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.53 | 0.77 | 24 | ACT |
| 2 | 109 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4TWJ · The structure of Sir2Af2 bound to a myristoylated histone peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O30124 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase 2 (O30124) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain B against A, TM-score 0.37
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 O30124
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 4TWJ · PDBe 4TWJ · UniProt O30124 · UniProt P02309
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