MolNFT v1 · #141960 · protein
Crystal structure of histone deacetylase 4 (HDAC4) in complex with a smrt corepressor SP2 fragment
5ZOP: “Crystal structure of histone deacetylase 4 (HDAC4) in complex with a smrt corepressor SP2 fragment”. X-ray diffraction, 2 ligands (K, ZN), 1 pocket (best druggability 0.39). MolNFT v1 #141960 on GenesisL1: 3D structure, binding…
- PDB
- 5ZOP
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 4; Smrt corepressor SP2 fragment
- EC
- 3.5.1.98
- UniProt
- P56524
- Ligands
- K, ZN
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Histone deacetylase 4 (EC 3.5.1.98) | protein | 383 | 41% helix, 13% strand | P56524 |
| A | Smrt corepressor SP2 fragment | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.39 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- G–A · 476 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ZOP · Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2… · the same entry in another collection · chain G against G, TM-score 1.00
- P56524 · AlphaFold monomer V2.0 prediction for histone deacetylase 4 (P56524) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 P56524
- Elsewhere: RCSB PDB 5ZOP · PDBe 5ZOP · UniProt P56524
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