Research workbench
Crystal structure of yeats domain of human YEATS2 in complex with H3K27BZ peptide
Analyse Crystal structure of yeats domain of human YEATS2 in complex with H3K27BZ… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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