MolNFT v1 · #138695 · protein
Crystal structure of LC3B in complex with FYCO1 lir
5WRD · Microtubule-associated proteins 1A/1B light chain 3B: “Crystal structure of LC3B in complex with FYCO1 lir”. X-ray diffraction, 2 pockets (best druggability 0.53). MolNFT v1 #138695 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WRD
- Type
- protein
- Length
- 272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microtubule-associated proteins 1A/1B light chain 3B; Peptide from fyve and coiled-coil…
- UniProt
- Q9CQV6, Q8VDC1
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Microtubule-associated proteins 1A/1B light chain 3B | protein | 117 | 32% helix, 23% strand | Q9CQV6 |
| C, D | Peptide from fyve and coiled-coil domain-containing protein 1 | protein | 19 | 47% helix, 11% strand | Q8VDC1 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 261 | 0.53 | 0.76 | 32 | empty |
| 2 | 132 | 0.45 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 974 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 925 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 921 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5WRD · Crystal structure of LC3B in complex with FYCO1 LIR · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CQV6 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q8VDC1 · AlphaFold monomer V2.0 prediction for fyve and coiled-coil domain- containing protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.52
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 Q9CQV6
- Every structure of UniProt Q8VDC1
- Elsewhere: RCSB PDB 5WRD · PDBe 5WRD · UniProt Q9CQV6 · UniProt Q8VDC1
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