Research workbench
Crystal structure analysis of human HDAC8 H143A variant complexed with substrate.
Analyse Crystal structure analysis of human HDAC8 H143A variant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EWF
- Type
- protein
- Length
- 1,472 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Peptidic substrate
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- ACE, MCM, K, ZN
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Histone deacetylase 8 (EC 3.5.1.98) | protein | 364 | 39% helix, 13% strand | Q9BY41 |
| I, J, K, L | Peptidic substrate | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains B, C, I, A, J, D, K, L
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · 4 copies · chains A, B, I, J, C, D, K, L
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, I, D, B, J, C, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.82 | 0.90 | 63 | ACE |
| 2 | 215 | 0.81 | 0.94 | 32 | MCM |
| 3 | 445 | 0.81 | 0.89 | 62 | empty |
| 4 | 312 | 0.80 | 0.91 | 36 | MCM |
| 5 | 159 | 0.74 | 0.92 | 33 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1017 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 0 hydrogen bonds · protein-protein
- B–J · 464 Ų buried · 10 hydrogen bonds · protein-protein
- D–L · 457 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, acetylation).
Compared structures
- 3EWF · Crystal Structure Analysis of human HDAC8 H143A variant complexed with substrate. · the same entry in another collection · chain L against L, TM-score 1.00
- Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain A against A, 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 Q9BY41
- Elsewhere: RCSB PDB 3EWF · PDBe 3EWF · UniProt Q9BY41
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.