MolNFT v1 · #50476 · protein
Crystal structure of L3MBTL1 protein in complex with mes
2RJC · LETHAL(3)MALIGNANT brain tumor-like protein: “Crystal structure of L3MBTL1 protein in complex with mes”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.78). MolNFT v1 #50476 on GenesisL1: 3D structure, binding…
- PDB
- 2RJC
- Type
- protein
- Length
- 933 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
- SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 313 | 19% helix, 30% strand | Q9Y468 |
| B | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 314 | 20% helix, 29% strand | Q9Y468 |
| C | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 306 | 20% helix, 30% strand | Q9Y468 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.78 | 0.80 | 109 | SO4, MES |
| 2 | 965 | 0.74 | 0.77 | 81 | empty |
| 3 | 767 | 0.72 | 0.78 | 66 | empty |
| 4 | 433 | 0.71 | 0.82 | 48 | empty |
| 5 | 168 | 0.55 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1071 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 281 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2RJC · Crystal structure of L3MBTL1 protein in complex with MES · 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 2RJC · PDBe 2RJC · UniProt Q9Y468
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.