MolNFT v1 · #171480 · protein
HDAC-DC
6Z6H · Histone deacetylase HDA1: “HDAC-DC”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #171480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z6H
- Type
- protein
- Length
- 4,774 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase HDA1; HDA1 complex subunit 2; HDA1 complex subunit 3,HDA1 complex…
- EC
- 3.5.1.98
- UniProt
- P53973, Q06629, Q06623
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 651 | 36% helix, 17% strand | P53973 |
| B, G | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 661 | 36% helix, 13% strand | P53973 |
| C, I | HDA1 complex subunit 2 | protein | 541 | 57% helix, 6% strand | Q06629 |
| D, J | HDA1 complex subunit 3,HDA1 complex subunit 3 | protein | 534 | 66% helix, 5% strand | Q06623 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.86 | 0.86 | 117 | empty |
| 2 | 1144 | 0.82 | 0.83 | 90 | empty |
| 3 | 322 | 0.81 | 0.91 | 42 | empty |
| 4 | 963 | 0.80 | 0.82 | 115 | empty |
| 5 | 86 | 0.78 | 0.99 | 21 | empty |
Interfaces
16 interfaces between chains.
- A–B · 5311 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 5140 Ų buried · 43 hydrogen bonds · protein-protein
- F–J · 2029 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2024 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2016 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 P53973
- Every structure of UniProt Q06629
- Every structure of UniProt Q06623
- Elsewhere: RCSB PDB 6Z6H · PDBe 6Z6H · UniProt P53973 · UniProt Q06629 · UniProt Q06623
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