MolNFT v1 · #138914 · protein
The YAF9 yeats domain recognizing H3K122SUC peptide
5WYI: “The YAF9 yeats domain recognizing H3K122SUC peptide”. X-ray diffraction, 1 ligand (SLL), 2 pockets (best druggability 0.41). MolNFT v1 #138914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WYI
- Type
- protein
- Length
- 420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YAF9; Ile-met-pro-lys-asp-ile-gln-leu
- UniProt
- B3LNW5
- Ligands
- SLL
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YAF9 | protein | 141 | 9% helix, 47% strand | B3LNW5 |
| B | YAF9 | protein | 138 | 9% helix, 49% strand | B3LNW5 |
| C | YAF9 | protein | 133 | 11% helix, 50% strand | B3LNW5 |
| E | Ile-met-pro-lys-asp-ile-gln-leu | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- SLL · (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid · ligand · chains C
- SIN · Succinic acid · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.41 | 0.75 | 23 | empty |
| 2 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–E · 469 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 131 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5WYI · The Yaf9 YEATS domain Recognizing H3K122suc Peptide · the same entry in another collection · chain A against A, 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 B3LNW5
- Elsewhere: RCSB PDB 5WYI · PDBe 5WYI · UniProt B3LNW5
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