MolNFT v1 · #141697 · protein
Crystal structure of SIRT3 in complex with H4K16BHB peptide
5ZGC · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Crystal structure of SIRT3 in complex with H4K16BHB peptide”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #141697 on GenesisL1: 3D…
- PDB
- 5ZGC
- Type
- protein
- Length
- 1,572 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Histone H4K16BHB peptide
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 263 | 41% helix, 18% strand | Q9NTG7 |
| B | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 258 | 41% helix, 20% strand | Q9NTG7 |
| C | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 262 | 41% helix, 17% strand | Q9NTG7 |
| D | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 260 | 40% helix, 16% strand | Q9NTG7 |
| E | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 273 | 43% helix, 18% strand | Q9NTG7 |
| F | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 212 | 44% helix, 15% strand | Q9NTG7 |
| G | Histone H4K16BHB peptide | protein | 11 | 0% helix, 18% strand | — |
| H | Histone H4K16BHB peptide | protein | 9 | 0% helix, 33% strand | — |
| I, K | Histone H4K16BHB peptide | protein | 7 | 0% helix, 29% strand | — |
| J, L | Histone H4K16BHB peptide | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.82 | 0.83 | 94 | empty |
| 2 | 907 | 0.74 | 0.78 | 87 | empty |
| 3 | 612 | 0.73 | 0.80 | 65 | empty |
| 4 | 71 | 0.72 | 0.96 | 23 | empty |
| 5 | 344 | 0.71 | 0.84 | 39 | empty |
Interfaces
17 interfaces between chains.
- A–G · 779 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 737 Ų buried · 13 hydrogen bonds · protein-protein
- C–I · 639 Ų buried · 12 hydrogen bonds · protein-protein
- D–K · 636 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 5ZGC · Crystal Structure of SIRT3 in complex with H4K16bhb peptide · the same entry in another collection · chain L against L, TM-score 1.00
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
- Elsewhere: RCSB PDB 5ZGC · PDBe 5ZGC · UniProt Q9NTG7
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