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Structure of human SIRT3 in complex with SRT1720 inhibitor
Analyse Structure of human SIRT3 in complex with SRT1720 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BN5
- Type
- protein
- Length
- 3,275 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- CNA, SR7, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 273 | 39% helix, 15% strand | Q9NTG7 |
| D | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 272 | 36% helix, 16% strand | Q9NTG7 |
Ligands and binding sites
- CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SR7 · N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D, F, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.87 | 0.88 | 103 | CNA, SR7 |
| 2 | 1131 | 0.87 | 0.88 | 110 | CNA, SR7 |
| 3 | 1127 | 0.87 | 0.88 | 111 | CNA, SR7 |
| 4 | 900 | 0.78 | 0.81 | 87 | empty |
| 5 | 897 | 0.77 | 0.80 | 90 | empty |
Interfaces
21 interfaces between chains.
- A–B · 700 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 636 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 630 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 590 Ų buried · 4 hydrogen bonds · protein-protein
- E–I · 530 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 4BN5 · Structure of human SIRT3 in complex with SRT1720 inhibitor · 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 4BN5 · PDBe 4BN5 · UniProt Q9NTG7
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