Research workbench
Structure and substrate binding properties of cobb, a SIR2 homolog protein deacetylase from eschericia COLI.
Analyse Structure and substrate binding properties of cobb, a SIR2 homolog protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5P
- Type
- protein
- Length
- 233 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase; Histone H4 (residues 12-19)
- EC
- 3.5.1.-
- UniProt
- P75960
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase (EC 3.5.1.-) | protein | 225 | 38% helix, 22% strand | P75960 |
| B | Histone H4 (residues 12-19) | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
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 | 339 | 0.74 | 0.86 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 703 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 1S5P · Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase… · the same entry in another collection · chain A against A, TM-score 1.00
- P75960 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase (P75960) · 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 P75960
- Elsewhere: RCSB PDB 1S5P · PDBe 1S5P · UniProt P75960
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