MolNFT v1 · #141486 · protein
Crystal structure of SIRT3 in complex with H3K4BHB peptide
5Z94 · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Crystal structure of SIRT3 in complex with H3K4BHB peptide”. X-ray diffraction, 2 ligands (ZN, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #141486 on GenesisL1: 3D…
- PDB
- 5Z94
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Gene for histone H3 (germline…
- EC
- 3.5.1.-
- UniProt
- Q9NTG7, V9H1G0
- Ligands
- ZN, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 273 | 43% helix, 19% strand | Q9NTG7 |
| C, D | Gene for histone H3 (germline gene) | protein | 7 | 0% helix, 43% strand | V9H1G0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.78 | 0.80 | 81 | GOL |
| 2 | 320 | 0.69 | 0.83 | 39 | empty |
| 3 | 337 | 0.69 | 0.82 | 47 | empty |
| 4 | 133 | 0.61 | 0.85 | 27 | empty |
| 5 | 152 | 0.58 | 0.82 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–D · 512 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 138 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5Z94 · Crystal Structure of SIRT3 in complex with H3K4bhb peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9NTG7
- Every structure of UniProt V9H1G0
- Elsewhere: RCSB PDB 5Z94 · PDBe 5Z94 · UniProt Q9NTG7 · UniProt V9H1G0
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