Research workbench
Crystal structure of danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with nexturastat a
Analyse Crystal structure of danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G0I
- Type
- protein
- Length
- 1,442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6
- UniProt
- F8W4B7
- Ligands
- N4R, K, ZN, CL
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 | protein | 722 | 43% helix, 13% strand | F8W4B7 |
| B | HDAC6 | protein | 720 | 44% helix, 14% strand | F8W4B7 |
Ligands and binding sites
- N4R · Nexturastat A · ligand · 4 copies · chains A, B
- K · Potassium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.59 | 0.84 | 28 | empty |
| 2 | 117 | 0.58 | 0.85 | 31 | EDO |
| 3 | 127 | 0.57 | 0.84 | 31 | EDO |
| 4 | 234 | 0.55 | 0.78 | 30 | empty |
| 5 | 86 | 0.54 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5G0I · Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with… · the same entry in another collection · 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 F8W4B7
- Elsewhere: RCSB PDB 5G0I · PDBe 5G0I · UniProt F8W4B7
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