Research workbench
Structure of kluyveromyces marxianus USB1 with uridine monophosphate
Analyse Structure of kluyveromyces marxianus USB1 with uridine monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PGL
- Type
- protein
- Length
- 642 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein YLR132C
- UniProt
- W0TCJ5
- Ligands
- U5P
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein YLR132C | protein | 218 | 40% helix, 28% strand | W0TCJ5 |
| B | Uncharacterized protein YLR132C | protein | 214 | 39% helix, 29% strand | W0TCJ5 |
| C | Uncharacterized protein YLR132C | protein | 210 | 40% helix, 29% strand | W0TCJ5 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, C
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains B, A, C
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.74 | 0.77 | 87 | GOL, PGE |
| 2 | 627 | 0.65 | 0.75 | 47 | U5P, PGE |
| 3 | 571 | 0.64 | 0.75 | 51 | U5P, PGE |
| 4 | 280 | 0.53 | 0.75 | 29 | U5P, EDO |
Interfaces
3 interfaces between chains.
- A–B · 791 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 391 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 343 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PGL · Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate · 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 6PGL · PDBe 6PGL · UniProt W0TCJ5
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