MolNFT v1 · #156077 · protein
Crystal structure of yeats domain of human YEATS2 in complex with H3K27BZ peptide
6LSD · Yeats domain-containing protein 2: “Crystal structure of yeats domain of human YEATS2 in complex with H3K27BZ peptide”. X-ray diffraction, 2 ligands (ACE, SO4), 1 pocket (best druggability 0.68). MolNFT v1 #156077 on GenesisL1: 3D…
- PDB
- 6LSD
- Type
- protein
- Length
- 281 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeats domain-containing protein 2; 2
- UniProt
- Q9ULM3
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yeats domain-containing protein 2 | protein | 130 | 7% helix, 53% strand | Q9ULM3 |
| B | Yeats domain-containing protein 2 | protein | 135 | 7% helix, 50% strand | Q9ULM3 |
| C, D | 2 | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.68 | 0.77 | 58 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 513 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 6LSD · Crystal Structure of YEATS domain of human YEATS2 in complex with H3K27bz peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ULM3 · AlphaFold monomer V2.0 prediction for yeats domain-containing protein 2 (Q9ULM3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9ULM3
- Elsewhere: RCSB PDB 6LSD · PDBe 6LSD · UniProt Q9ULM3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.