Research workbench
Crystal structure of SIRT2 in complex with the macrocyclic peptide S2IL5
Analyse Crystal structure of SIRT2 in complex with the macrocyclic peptide S2IL5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L3O
- Type
- protein
- Length
- 1,235 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Cyclic peptide S2IL5
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- ZN, NH2
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 297 | 38% helix, 17% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 295 | 36% helix, 18% strand | Q8IXJ6 |
| C | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 294 | 36% helix, 17% strand | Q8IXJ6 |
| D | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 293 | 36% helix, 18% strand | Q8IXJ6 |
| E, F, G, H | Cyclic peptide S2IL5 | protein | 14 | 0% helix, 21% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NH2 · Amino group · ion · 4 copies · chains E, F, G, H
- ACY · Acetic acid · additive · 4 copies · chains A, E, B, F, C, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.77 | 0.92 | 35 | empty |
| 2 | 196 | 0.74 | 0.90 | 32 | empty |
| 3 | 171 | 0.74 | 0.91 | 32 | empty |
| 4 | 177 | 0.73 | 0.91 | 34 | empty |
| 5 | 276 | 0.53 | 0.75 | 29 | empty |
Interfaces
9 interfaces between chains.
- D–H · 983 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 982 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 969 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 961 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 modified (additive adduct, nonstandard).
Compared structures
- 4L3O · Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 · the same entry in another collection · chain E against E, TM-score 1.00
- Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q8IXJ6
- Elsewhere: RCSB PDB 4L3O · PDBe 4L3O · UniProt Q8IXJ6
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