MolNFT v1 · #171483 · protein + DNA
HDAC-PC-NUC
6Z6P · Histone deacetylase HDA1: “HDAC-PC-NUC”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #171483 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z6P
- Type
- protein + DNA
- Length
- 3,428 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase HDA1; HDA1 complex subunit 3,HDA1 complex subunit 3; HDA1 complex…
- EC
- 3.5.1.98
- UniProt
- P53973, Q06623, Q06629, A0A310TTQ1, P62799, Q6AZJ8, A0A1L8FQA5, P84233, P06897, A0A1L8FQ56
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 14 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 651 | 33% helix, 15% strand | P53973 |
| L | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 661 | 33% helix, 13% strand | P53973 |
| M | HDA1 complex subunit 3,HDA1 complex subunit 3 | protein | 534 | 60% helix, 3% strand | Q06623 |
| N | HDA1 complex subunit 2 | protein | 541 | 52% helix, 5% strand | Q06629 |
| A | Histone H3 | protein | 97 | 64% helix, 2% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 83 | 54% helix, 4% strand | P62799 |
| C | Histone H2A | protein | 103 | 52% helix, 4% strand | Q6AZJ8 |
| D | Histone H2B | protein | 95 | 72% helix, 2% strand | A0A1L8FQA5 |
| E | Histone H3.2 | protein | 97 | 63% helix, 3% strand | P84233 |
| F | Histone H4 | protein | 78 | 58% helix, 6% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 46% helix, 2% strand | P06897 |
| H | Histone H2B | protein | 93 | 75% helix, 1% strand | A0A1L8FQ56 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains K, L
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 | 1169 | 0.86 | 0.87 | 123 | empty |
| 2 | 1085 | 0.85 | 0.86 | 153 | empty |
| 3 | 425 | 0.81 | 0.89 | 81 | empty |
| 4 | 805 | 0.80 | 0.83 | 76 | empty |
| 5 | 129 | 0.79 | 0.97 | 23 | empty |
Interfaces
49 interfaces between chains.
- I–J · 6712 Ų buried · 861 hydrogen bonds · nucleic-nucleic
- K–L · 5534 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 2532 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2508 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2494 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6Z6P · HDAC-PC-Nuc · the same entry in another collection · chain J against J, 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 P53973
- Every structure of UniProt Q06623
- Every structure of UniProt Q06629
- Every structure of UniProt A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt A0A1L8FQA5
- Every structure of UniProt P84233
- Every structure of UniProt P06897
- Every structure of UniProt A0A1L8FQ56
- Elsewhere: RCSB PDB 6Z6P · PDBe 6Z6P · UniProt P53973 · UniProt Q06623 · UniProt Q06629 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQA5 · UniProt P84233 · UniProt P06897 · UniProt A0A1L8FQ56
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