Research workbench
Structure of Kluyveromyces marxianus Usb1
Analyse Structure of Kluyveromyces marxianus Usb1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PFQ
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)
- Molecule
- Uncharacterized protein YLR132C
- UniProt
- W0TCJ5
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Uncharacterized protein YLR132C | protein | 212 | 40% helix, 29% strand | W0TCJ5 |
| A | Uncharacterized protein YLR132C | protein | 216 | 39% helix, 28% strand | W0TCJ5 |
| B | Uncharacterized protein YLR132C | protein | 212 | 37% helix, 29% strand | W0TCJ5 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.74 | 0.77 | 104 | GOL |
| 2 | 291 | 0.59 | 0.78 | 26 | GOL |
| 3 | 282 | 0.57 | 0.77 | 27 | GOL |
| 4 | 165 | 0.52 | 0.79 | 22 | GOL |
| 5 | 108 | 0.45 | 0.79 | 28 | empty |
Interfaces
3 interfaces between chains.
- C–A · 740 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 323 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 175 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6PFQ · Structure of kluyveromyces marxianus USB1 · 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 W0TCJ5
- Elsewhere: RCSB PDB 6PFQ · PDBe 6PFQ · UniProt W0TCJ5
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