Research workbench
Crystal structure of udp-glucose pyrophosphorylase from sugarcane
Analyse Crystal structure of udp-glucose pyrophosphorylase from sugarcane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WEG
- Type
- protein
- Length
- 907 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- A0A075E2Q1
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 455 | 33% helix, 28% strand | A0A075E2Q1 |
| B | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 452 | 34% helix, 28% strand | A0A075E2Q1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.74 | 0.78 | 95 | SO4 |
| 2 | 699 | 0.68 | 0.76 | 90 | SO4 |
| 3 | 216 | 0.62 | 0.82 | 25 | empty |
| 4 | 204 | 0.62 | 0.82 | 24 | empty |
| 5 | 63 | 0.49 | 0.84 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5WEG · Crystal Structure of UDP-glucose pyrophosphorylase from Sugarcane · 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 A0A075E2Q1
- Elsewhere: RCSB PDB 5WEG · PDBe 5WEG · UniProt A0A075E2Q1
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