MolNFT v1 · #136810 · protein
Crystal structure of NEDD4 lir-fused human LC3B_2-119
5V4K · Microtubule-associated proteins 1A/1B light chain 3B…: “Crystal structure of NEDD4 lir-fused human LC3B_2-119”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.27). MolNFT v1 #136810 on GenesisL1: 3D structure…
- PDB
- 5V4K
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microtubule-associated proteins 1A/1B light chain 3B, microtubule-associated proteins…
- UniProt
- Q9GZQ8
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microtubule-associated proteins 1A/1B light chain 3B, microtubule-associated proteins 1A/1B light chain 3B,MICROTUBULE- associated proteins 1A/1B light chain 3B | protein | 125 | 30% helix, 22% strand | Q9GZQ8 |
| B | Microtubule-associated proteins 1A/1B light chain 3B, microtubule-associated proteins 1A/1B light chain 3B,MICROTUBULE- associated proteins 1A/1B light chain 3B | protein | 124 | 31% helix, 22% strand | Q9GZQ8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5V4K · Crystal structure of NEDD4 LIR-fused human LC3B_2-119 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZQ8 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q9GZQ8
- Elsewhere: RCSB PDB 5V4K · PDBe 5V4K · UniProt Q9GZQ8
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