MolNFT v1 · #106693 · protein
Crystal structure of AF9 yeats bound to H3K9AC peptide
4TMP · Protein af-9: “Crystal structure of AF9 yeats bound to H3K9AC peptide”. X-ray diffraction, 1 pocket (best druggability 0.29). MolNFT v1 #106693 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TMP
- Type
- protein
- Length
- 293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein af-9; Ala-arg-thr-lys-gln-thr-ala-arg-aly-ser-thr
- UniProt
- P42568, P84243
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein af-9 | protein | 138 | 11% helix, 54% strand | P42568 |
| B, D | Ala-arg-thr-lys-gln-thr-ala-arg-aly-ser-thr | protein | 8 | 0% helix, 25% strand | P84243 |
| C | Protein af-9 | protein | 139 | 11% helix, 53% strand | P42568 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.29 | 0.74 | 16 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 748 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 4TMP · Crystal structure of AF9 YEATS bound to H3K9ac peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P42568 · AlphaFold monomer V2.0 prediction for protein af-9 (P42568) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain B against A, TM-score 0.41
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 P42568
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 4TMP · PDBe 4TMP · UniProt P42568 · UniProt P84243
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