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Crystal structure of L3MBTL1 in complex with H4K20ME2 (residues 17- 25), trigonal form
Analyse Crystal structure of L3MBTL1 in complex with H4K20ME2 (residues 17- 25)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PQW
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LETHAL(3)MALIGNANT brain tumor-like protein; Histone H4
- UniProt
- Q9Y468
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 315 | 20% helix, 29% strand | Q9Y468 |
| B | Histone H4 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · 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 | 817 | 0.73 | 0.78 | 71 | empty |
Interfaces
1 interface between chains.
- A–B · 221 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 2PQW · Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y468 · AlphaFold monomer V2.0 prediction for LETHAL(3)MALIGNANT brain tumor- like protein 1… · 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 Q9Y468
- Elsewhere: RCSB PDB 2PQW · PDBe 2PQW · UniProt Q9Y468
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