Research workbench
Crystal structure of the 3-mbt domain from human L3MBTL1 in complex with P53K382ME1
Analyse Crystal structure of the 3-mbt domain from human L3MBTL1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OQ5
- Type
- protein
- Length
- 927 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LETHAL(3)MALIGNANT brain tumor-like protein
- UniProt
- Q9Y468
- Ligands
- MLZ
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 309 | 16% helix, 29% strand | Q9Y468 |
Ligands and binding sites
- MLZ · N-methyl-lysine · ligand · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.72 | 0.81 | 41 | empty |
| 2 | 782 | 0.71 | 0.77 | 60 | empty |
| 3 | 481 | 0.71 | 0.81 | 50 | empty |
| 4 | 122 | 0.51 | 0.80 | 24 | empty |
| 5 | 112 | 0.46 | 0.79 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 619 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OQ5 · Crystal structure of the 3-MBT domain from human L3MBTL1 in complex with p53K382me1 · 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 C against A, TM-score 0.98
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 3OQ5 · PDBe 3OQ5 · UniProt Q9Y468
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