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Crystal structure of the ligand-binding domain of L. thermotolerans UPC2 in complex with ergosterol
Analyse Crystal structure of the ligand-binding domain of L. thermotolerans UPC2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VPU
- Type
- protein
- Length
- 1,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol uptake control protein 2 (UPC2)
- UniProt
- C5DKV6
- Ligands
- ERG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol uptake control protein 2 (UPC2) | protein | 275 | 58% helix, 0% strand | C5DKV6 |
| B | Sterol uptake control protein 2 (UPC2) | protein | 266 | 66% helix, 0% strand | C5DKV6 |
| C | Sterol uptake control protein 2 (UPC2) | protein | 269 | 60% helix, 0% strand | C5DKV6 |
| D | Sterol uptake control protein 2 (UPC2) | protein | 266 | 65% helix, 0% strand | C5DKV6 |
Ligands and binding sites
- ERG · Ergosterol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.83 | 0.92 | 37 | ERG |
| 2 | 376 | 0.82 | 0.90 | 38 | ERG |
| 3 | 381 | 0.82 | 0.90 | 42 | ERG |
| 4 | 376 | 0.80 | 0.89 | 44 | ERG |
| 5 | 472 | 0.64 | 0.77 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 874 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 815 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 667 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VPU · Crystal structure of the ligand-binding domain of L. thermotolerans Upc2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 C5DKV6
- Elsewhere: RCSB PDB 7VPU · PDBe 7VPU · UniProt C5DKV6
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