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
- 6WHO
- Type
- protein
- Length
- 1,128 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2; U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- NA, ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 374 | 41% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 41% helix, 12% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 365 | 40% helix, 12% strand | Q92769 |
| F, G | U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle | protein | 8 | 0% helix, 0% strand | — |
| H | U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle | protein | 7 | 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
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.72 | 0.79 | 64 | PG4, PGE |
| 2 | 604 | 0.66 | 0.76 | 50 | empty |
| 3 | 182 | 0.52 | 0.78 | 20 | empty |
| 4 | 73 | 0.39 | 0.79 | 21 | empty |
| 5 | 63 | 0.33 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 701 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 558 Ų buried · 12 hydrogen bonds · protein-protein
- C–H · 451 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 420 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 411 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 d-amino, 1 covalent (nonstandard, D-amino acid, additive adduct).
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 6WHO · PDBe 6WHO · UniProt Q92769
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