Research workbench
Crystal structure of T7-tagged optineurin lir-fused human LC3B_2-119
Analyse Crystal structure of T7-tagged optineurin lir-fused human LC3B_2-119 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTW
- Type
- protein
- Length
- 375 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Optineurin, microtubule-associated proteins 1A/1B light chain 3B
- UniProt
- Q96CV9, Q9GZQ8
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Optineurin, microtubule-associated proteins 1A/1B light chain 3B | protein | 125 | 30% helix, 22% strand | Q96CV9, Q9GZQ8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.61 | 0.83 | 34 | SO4 |
| 2 | 308 | 0.55 | 0.76 | 50 | empty |
| 3 | 102 | 0.39 | 0.76 | 23 | empty |
| 4 | 52 | 0.34 | 0.78 | 14 | empty |
| 5 | 65 | 0.29 | 0.73 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 528 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VTW · Crystal structure of T7-tagged Optineurin 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 A against A, TM-score 0.88
- Q96CV9 · AlphaFold monomer V2.0 prediction for optineurin (Q96CV9) · a predicted model of the same protein · chain A against A, TM-score 0.21
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 Q96CV9
- Every structure of UniProt Q9GZQ8
- Elsewhere: RCSB PDB 3VTW · PDBe 3VTW · UniProt Q96CV9 · UniProt Q9GZQ8
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