MolNFT v1 · #168470 · protein
Histone deacetylases complex with peptide macrocycles
6WHN · Histone deacetylase 2: “Histone deacetylases complex with peptide macrocycles”. X-ray diffraction, 2 ligands (NA, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #168470 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WHN
- Type
- protein
- Length
- 1,133 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2; U2M-asn-pro-lys-gln-dly-TRP-gly peptide macrocycle
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- NA, ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 375 | 40% helix, 13% strand | Q92769 |
| B, C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 367 | 41% helix, 13% strand | Q92769 |
| F, G, H | U2M-asn-pro-lys-gln-dly-TRP-gly peptide macrocycle | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, F, B, G, C, H
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.73 | 0.77 | 82 | PG4, PGE |
| 2 | 617 | 0.68 | 0.77 | 51 | NHE |
| 3 | 126 | 0.42 | 0.76 | 21 | empty |
| 4 | 55 | 0.34 | 0.78 | 17 | empty |
| 5 | 53 | 0.26 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 417 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 413 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 400 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 d-amino, 3 modified (D-amino acid, nonstandard).
Compared structures
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 Q92769
- Elsewhere: RCSB PDB 6WHN · PDBe 6WHN · UniProt Q92769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.