Research workbench
Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from candida albicans, in the substrate-binding form
Analyse Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YQH
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine pyrophosphorylase
- EC
- 2.7.7.23
- UniProt
- O74933
- Ligands
- GN1, MG, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) | protein | 472 | 39% helix, 22% strand | O74933 |
| B | Udp-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) | protein | 466 | 39% helix, 22% strand | O74933 |
Ligands and binding sites
- GN1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.70 | 0.79 | 49 | GN1 |
| 2 | 422 | 0.65 | 0.78 | 43 | GN1 |
| 3 | 481 | 0.64 | 0.77 | 40 | empty |
| 4 | 209 | 0.53 | 0.77 | 29 | empty |
| 5 | 246 | 0.52 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 215 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2YQH · Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida… · the same entry in another collection · chain A against A, TM-score 1.00
- O74933 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine pyrophosphorylase (O74933) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O74933
- Elsewhere: RCSB PDB 2YQH · PDBe 2YQH · UniProt O74933
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