MolNFT v1 · #139908 · protein
Crystal structure of GAS41 yeats bound to H3K27AC peptide
5XTZ · Yeats domain-containing protein 4: “Crystal structure of GAS41 yeats bound to H3K27AC peptide”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #139908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XTZ
- Type
- protein
- Length
- 570 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeats domain-containing protein 4; Thr-lys-ala-ala-arg-aly-ser-ala-pro-ala
- UniProt
- O95619
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yeats domain-containing protein 4 | protein | 139 | 9% helix, 50% strand | O95619 |
| B | Yeats domain-containing protein 4 | protein | 132 | 8% helix, 51% strand | O95619 |
| C | Yeats domain-containing protein 4 | protein | 138 | 8% helix, 49% strand | O95619 |
| D | Yeats domain-containing protein 4 | protein | 151 | 9% helix, 46% strand | O95619 |
| E | Thr-lys-ala-ala-arg-aly-ser-ala-pro-ala | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.69 | 0.80 | 43 | ACT |
| 2 | 229 | 0.47 | 0.73 | 31 | empty |
| 3 | 168 | 0.44 | 0.74 | 27 | empty |
| 4 | 125 | 0.42 | 0.76 | 18 | empty |
| 5 | 55 | 0.27 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–D · 823 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 392 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 5XTZ · Crystal structure of GAS41 YEATS bound to H3K27ac peptide · the same entry in another collection · chain E against E, TM-score 1.00
- O95619 · AlphaFold monomer V2.0 prediction for yeats domain-containing protein 4 (O95619) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O95619
- Elsewhere: RCSB PDB 5XTZ · PDBe 5XTZ · UniProt O95619
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