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Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070
Analyse Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B31
- Type
- protein
- Length
- 577 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Thermocrispum agreste DSM 44070
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- A0A2W4LV58
- Ligands
- K, SCN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.75 · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 288 | 41% helix, 25% strand | A0A2W4LV58 |
| B | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 289 | 41% helix, 25% strand | A0A2W4LV58 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 73 | 0.76 | 0.98 | 17 | EDO |
| 2 | 613 | 0.67 | 0.76 | 64 | EDO, K |
| 3 | 565 | 0.66 | 0.77 | 63 | EDO |
| 4 | 412 | 0.57 | 0.74 | 57 | SCN |
| 5 | 144 | 0.44 | 0.75 | 22 | K |
Interfaces
1 interface between chains.
- A–B · 2364 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
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 A0A2W4LV58
- Elsewhere: RCSB PDB 8B31 · PDBe 8B31 · UniProt A0A2W4LV58
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