MolNFT v1 · #74840 · protein
Crystal structure of L3MBTL1 (mbt repeat) in complex with a nicotinamide antagonist
3P8H · LETHAL(3)MALIGNANT brain tumor-like protein: “Crystal structure of L3MBTL1 (mbt repeat) in complex with a nicotinamide antagonist”. X-ray diffraction, 2 ligands (P8H, SO4), 9 pockets (best druggability 0.76). MolNFT v1 #74840 on…
- PDB
- 3P8H
- Type
- protein
- Length
- 935 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
- P8H, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 313 | 20% helix, 29% strand | Q9Y468 |
| B | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 310 | 19% helix, 30% strand | Q9Y468 |
| C | LETHAL(3)MALIGNANT brain tumor-like protein | protein | 312 | 20% helix, 29% strand | Q9Y468 |
Ligands and binding sites
- P8H · 3-bromo-5-[(4-pyrrolidin-1-ylpiperidin-1-yl)carbonyl]pyridine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.76 | 0.79 | 71 | empty |
| 2 | 1017 | 0.72 | 0.76 | 91 | SO4 |
| 3 | 754 | 0.72 | 0.78 | 71 | empty |
| 4 | 625 | 0.66 | 0.75 | 48 | P8H |
| 5 | 55 | 0.34 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 494 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 270 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3P8H · Crystal structure of L3MBTL1 (MBT repeat) in complex with a nicotinamide antagonist · the same entry in another collection · chain C against C, 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 3P8H · PDBe 3P8H · UniProt Q9Y468
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