MolNFT v1 · #144590 · protein
Crystal structure of L3MBTL1 mbt domain with MBK14970
6BYB · LETHAL(3)MALIGNANT brain tumor-like protein 1: “Crystal structure of L3MBTL1 mbt domain with MBK14970”. X-ray diffraction, 2 ligands (EC7, UNX), 2 pockets (best druggability 0.70). MolNFT v1 #144590 on GenesisL1: 3D structure…
- PDB
- 6BYB
- Type
- protein
- Length
- 310 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LETHAL(3)MALIGNANT brain tumor-like protein 1
- UniProt
- Q9Y468
- Ligands
- EC7, UNX
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LETHAL(3)MALIGNANT brain tumor-like protein 1 | protein | 310 | 21% helix, 29% strand | Q9Y468 |
Ligands and binding sites
- EC7 · (S)-N-(cyclopropylmethyl)-N~2~-methyl-N-[2-methyl-2-(1-methylpiperidin-4-yl)propyl]alaninamide · ligand · chains A
- UNX · Unknown atom or ion · ion · 13 copies · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.70 | 0.77 | 52 | UNX |
| 2 | 60 | 0.31 | 0.76 | 12 | empty |
Compared structures
- 6BYB · Crystal structure of L3MBTL1 MBT Domain with MBK14970 · 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 6BYB · PDBe 6BYB · UniProt Q9Y468
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