MolNFT v1 · #141169 · protein
Crystal structure of AF9 yeats domain in complex with a peptide inhibitor "phq-H3(Q5-K9)" modified at K9 with 2-furancarboyl group
5YYF · Protein af-9: “Crystal structure of AF9 yeats domain in complex with a peptide inhibitor "phq-H3(Q5-K9)" modified at K9 with…”. X-ray diffraction, 4 ligands (PHQ, FOA, SO4), 3 pockets (best druggability 0.57). MolNFT v1 #141169 on…
- PDB
- 5YYF
- Type
- protein
- Length
- 287 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein af-9; Peptide inhibitor phq-H3(Q5-K9)
- UniProt
- P42568
- Ligands
- PHQ, FOA, SO4, NH2
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein af-9 | protein | 138 | 7% helix, 51% strand | P42568 |
| B, D | Peptide inhibitor phq-H3(Q5-K9) | protein | 5 | 0% helix, 20% strand | — |
| C | Protein af-9 | protein | 139 | 9% helix, 50% strand | P42568 |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, B, C, D
- FOA · 2-furoic acid · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- NH2 · Amino group · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.57 | 0.79 | 36 | empty |
| 2 | 61 | 0.31 | 0.75 | 12 | empty |
| 3 | 59 | 0.30 | 0.75 | 15 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 427 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 422 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5YYF · Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)"… · 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
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
- Elsewhere: RCSB PDB 5YYF · PDBe 5YYF · UniProt P42568
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