Research workbench
Crystal structure of a domain-swapped dimer of the second starkin domain of LAM2
Analyse Crystal structure of a domain-swapped dimer of the second starkin domain of LAM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQQ
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-anchored lipid-binding protein YSP2
- UniProt
- Q06681
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-anchored lipid-binding protein YSP2 | protein | 159 | 31% helix, 42% strand | Q06681 |
| B | Membrane-anchored lipid-binding protein YSP2 | protein | 159 | 30% helix, 43% strand | Q06681 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.70 | 0.83 | 38 | empty |
| 2 | 235 | 0.69 | 0.85 | 35 | empty |
| 3 | 292 | 0.65 | 0.81 | 53 | empty |
| 4 | 76 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2986 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5YQQ · Crystal structure of a domain-swapped dimer of the second StARkin domain of Lam2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q06681 · AlphaFold monomer V2.0 prediction for membrane-anchored lipid-binding protein YSP2… · a predicted model of the same protein · chain B against A, TM-score 0.77
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 Q06681
- Elsewhere: RCSB PDB 5YQQ · PDBe 5YQQ · UniProt Q06681
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