Research workbench
Human SIRT3 Recognizing H3K4cr
Analyse Human SIRT3 Recognizing H3K4cr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ISO
- Type
- protein
- Length
- 1,535 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.95
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Arg-thr-lys-gln-thr-ala-arg
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- CRD, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.95 · 8 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 270 | 43% helix, 19% strand | Q9NTG7 |
| C, D, F, H, J | Arg-thr-lys-gln-thr-ala-arg | protein | 7 | 0% helix, 43% strand | — |
| B | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 264 | 41% helix, 19% strand | Q9NTG7 |
| E | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 263 | 43% helix, 19% strand | Q9NTG7 |
| G | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 255 | 44% helix, 20% strand | Q9NTG7 |
| L | Arg-thr-lys-gln-thr-ala-arg | protein | 6 | 0% helix, 33% strand | — |
| I | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 248 | 43% helix, 21% strand | Q9NTG7 |
| K | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 194 | 40% helix, 16% strand | Q9NTG7 |
Ligands and binding sites
- CRD · (2E)-but-2-enal · ligand · 6 copies · chains A, C, B, D, E, F, H, G, L, K, I, J
- ZN · Zinc ion · metal · 5 copies · chains A, B, E, G, I
- GOL · Glycerol · additive · 4 copies · chains B, E, G, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.78 | 0.81 | 85 | empty |
| 2 | 267 | 0.77 | 0.90 | 41 | CRD |
| 3 | 309 | 0.77 | 0.88 | 33 | GOL, CRD |
| 4 | 1050 | 0.75 | 0.78 | 103 | empty |
| 5 | 687 | 0.69 | 0.76 | 52 | CRD, GOL |
Interfaces
20 interfaces between chains.
- H–G · 568 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 7 hydrogen bonds · protein-protein
- L–K · 525 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 508 Ų buried · 7 hydrogen bonds · protein-protein
- B–I · 479 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6ISO · Human SIRT3 recognizing H3K4CR · 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 6ISO · PDBe 6ISO · UniProt Q9NTG7
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