MolNFT v1 · #120027 · protein
LC3B-FUNDC1 complex
5GMV · Microtubule-associated proteins 1A/1B light chain 3B: “LC3B-FUNDC1 complex”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #120027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GMV
- Type
- protein
- Length
- 256 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 FUN14…
- UniProt
- Q9GZQ8, Q8IVP5
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Microtubule-associated proteins 1A/1B light chain 3B | protein | 120 | 38% helix, 22% strand | Q9GZQ8 |
| D, C | Peptide from FUN14 domain-containing protein 1 | protein | 8 | 0% helix, 25% strand | Q8IVP5 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.70 | 0.76 | 58 | empty |
| 2 | 52 | 0.29 | 0.75 | 12 | empty |
| 3 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 647 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 623 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 103 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5GMV · LC3B-FUNDC1 complex · the same entry in another collection · chain B against B, 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 0.97
- Q8IVP5 · AlphaFold monomer V2.0 prediction for FUN14 domain-containing protein 1 (Q8IVP5) · a predicted model of the same protein · chain D against A, TM-score 0.37
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
- Every structure of UniProt Q8IVP5
- Elsewhere: RCSB PDB 5GMV · PDBe 5GMV · UniProt Q9GZQ8 · UniProt Q8IVP5
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