Research workbench
NUA4 hat module bound to the nucleosome
Analyse NUA4 hat module bound to the nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VVU
- Type
- protein + DNA
- Length
- 1,825 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromatin modification-related protein EAF6; Chromatin modification-related protein YNG2…
- EC
- 2.3.1.48
- UniProt
- A0A6A5PYU5, P38806, P43572, A0A6A5Q414
- Ligands
- CMC
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 14 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Chromatin modification-related protein EAF6 | protein | 46 | 96% helix, 0% strand | A0A6A5PYU5 |
| V | Chromatin modification-related protein YNG2 | protein | 113 | 89% helix, 0% strand | P38806 |
| T | Enhancer of polycomb-like protein 1 | protein | 274 | 55% helix, 1% strand | P43572 |
| O | H3 | protein | 96 | 67% helix, 4% strand | — |
| Q | H4 | protein | 80 | 64% helix, 9% strand | — |
| S, N | H2A | protein | 106 | 57% helix, 7% strand | — |
| U | H2B | protein | 92 | 75% helix, 4% strand | — |
| A | H3 | protein | 94 | 68% helix, 4% strand | — |
| B | H4 | protein | 87 | 61% helix, 8% strand | — |
| D | H2B | protein | 93 | 75% helix, 4% strand | — |
| P | Histone acetyltransferase ESA1 (EC 2.3.1.48) | protein | 270 | 37% helix, 22% strand | A0A6A5Q414 |
| W | DNA (207-mer) | dna | 180 | — | — |
| I | DNA (207-mer) | dna | 179 | — | — |
| X | Enhancer of polycomb-like protein 1 | protein | 9 | 0% helix, 0% strand | P43572 |
Ligands and binding sites
- CMC · Carboxymethyl coenzyme *A · ligand · chains B, P
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 | 1125 | 0.79 | 0.81 | 99 | empty |
| 2 | 805 | 0.77 | 0.81 | 90 | empty |
| 3 | 469 | 0.75 | 0.84 | 54 | empty |
| 4 | 323 | 0.75 | 0.87 | 41 | CMC |
| 5 | 396 | 0.74 | 0.85 | 42 | empty |
Interfaces
48 interfaces between chains.
- W–I · 8054 Ų buried · 658 hydrogen bonds · nucleic-nucleic
- T–P · 3219 Ų buried · 63 hydrogen bonds · protein-protein
- V–T · 2869 Ų buried · 34 hydrogen bonds · protein-protein
- N–D · 2607 Ų buried · 21 hydrogen bonds · protein-protein
- S–U · 2581 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7VVU · NuA4 HAT module bound to the nucleosome · the same entry in another collection · chain X against X, 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 A0A6A5PYU5
- Every structure of UniProt P38806
- Every structure of UniProt P43572
- Every structure of UniProt A0A6A5Q414
- Elsewhere: RCSB PDB 7VVU · PDBe 7VVU · UniProt A0A6A5PYU5 · UniProt P38806 · UniProt P43572 · UniProt A0A6A5Q414
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.