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
- 6WHZ
- Type
- protein
- Length
- 1,125 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2; U2M-asn-hyp-lys-gln-dly-TRP-gly peptide macrocycle
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- NA, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 4 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 | 38% helix, 12% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 364 | 40% helix, 12% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 365 | 39% helix, 12% strand | Q92769 |
| D, F, G | U2M-asn-hyp-lys-gln-dly-TRP-gly peptide macrocycle | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, D, B, F, C, G
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.73 | 0.78 | 78 | PGE |
| 2 | 649 | 0.69 | 0.78 | 61 | empty |
| 3 | 141 | 0.45 | 0.76 | 21 | empty |
| 4 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–C · 759 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 439 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 395 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 379 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 3 d-amino (D-amino acid, hydroxylation, 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 6WHZ · PDBe 6WHZ · UniProt Q92769
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