Research workbench
Crystal structure of L3MBTL1 in complex with H4K20ME2 (residues 12- 30), orthorhombic form I
Analyse Crystal structure of L3MBTL1 in complex with H4K20ME2 (residues 12- 30)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RJF
- Type
- protein
- Length
- 964 residues
- Chains
- 5
- 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
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 315 | 20% helix, 31% strand | Q9Y468 |
| B | Histone H4 | protein | 10 | 0% helix, 30% strand | — |
| D | Histone H4 | protein | 9 | 0% helix, 33% strand | — |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.74 | 0.82 | 55 | empty |
| 2 | 829 | 0.73 | 0.78 | 65 | empty |
| 3 | 672 | 0.73 | 0.80 | 61 | empty |
| 4 | 778 | 0.72 | 0.77 | 65 | empty |
| 5 | 798 | 0.72 | 0.77 | 63 | empty |
Interfaces
7 interfaces between chains.
- C–E · 979 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 293 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 287 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2RJF · Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 12-30), orthorhombic 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 2RJF · PDBe 2RJF · UniProt Q9Y468
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