Research workbench
Crystal structure of L3MBTL1 in complex with H4K20ME2 (residues 17- 25), orthorhombic form II
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
- 2RJE
- Type
- protein
- Length
- 951 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
- Ligands
- CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 309 | 20% helix, 29% strand | Q9Y468 |
| B | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 313 | 20% helix, 29% strand | Q9Y468 |
| C | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 312 | 19% helix, 29% strand | Q9Y468 |
| P | Histone H4 | protein | 9 | 0% helix, 33% strand | — |
| Q | Histone H4 | protein | 8 | 0% helix, 38% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.76 | 0.81 | 69 | empty |
| 2 | 802 | 0.76 | 0.80 | 61 | empty |
| 3 | 788 | 0.72 | 0.78 | 62 | empty |
| 4 | 433 | 0.72 | 0.82 | 49 | empty |
| 5 | 645 | 0.71 | 0.79 | 54 | empty |
Interfaces
7 interfaces between chains.
- B–C · 962 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 483 Ų buried · 11 hydrogen bonds · protein-protein
- P–Q · 398 Ų buried · 7 hydrogen bonds · protein-protein
- B–Q · 302 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2RJE · Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), orthorhombic form… · the same entry in another collection · chain Q against Q, 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 2RJE · PDBe 2RJE · UniProt Q9Y468
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.