MolNFT v1 · #22467 · protein

Crystal structure of human HDAC8 complexed with trichostatin a

1T64 · Histone deacetylase 8: “Crystal structure of human HDAC8 complexed with trichostatin a”. X-ray diffraction, 4 ligands (TSN, CA, NA), 3 pockets (best druggability 0.73). MolNFT v1 #22467 on GenesisL1: 3D structure, binding sites and…

PDB: 1T64
Type: protein
Length: 728 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 8
UniProt: Q9BY41
Ligands: TSN, CA, NA, ZN
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Histone deacetylase 8	protein	364	40% helix, 13% strand	Q9BY41

Ligands and binding sites

TSN · Trichostatin A · ligand · 4 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
NA · Sodium ion · metal · 4 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.73	0.77	76	empty
2	141	0.70	0.90	34	TSN
3	101	0.64	0.89	22	TSN

Interfaces

1 interface between chains.

A–B · 371 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1T64 · Crystal Structure of human HDAC8 complexed with Trichostatin A · the same entry in another collection · chain A against A, 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 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 Q9BY41
Elsewhere: RCSB PDB 1T64 · PDBe 1T64 · UniProt Q9BY41

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