Research workbench
Histone deacetylases complex with peptide macrocycles
Analyse Histone deacetylases complex with peptide macrocycles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WI3
- Type
- protein
- Length
- 1,124 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2; (SHA)W(DTH)DN(DSN)(DME)(DAS)K peptide macrocycle
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- NA, ZN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 372 | 39% helix, 12% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 40% helix, 12% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 365 | 40% helix, 12% strand | Q92769 |
| F, G | (SHA)W(DTH)DN(DSN)(DME)(DAS)K peptide macrocycle | protein | 9 | 0% helix, 0% strand | — |
| H | (SHA)W(DTH)DN(DSN)(DME)(DAS)K peptide macrocycle | protein | 3 | 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
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.72 | 0.79 | 70 | PG4, PGE |
| 2 | 571 | 0.66 | 0.76 | 53 | empty |
| 3 | 202 | 0.53 | 0.78 | 23 | empty |
| 4 | 73 | 0.29 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 692 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 439 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 412 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 6WI3 · PDBe 6WI3 · UniProt Q92769
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