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Crystal structure of udp-N-acetylglucosamine pyrophosphorylase (AGX2) from mus musculus at 2.50 a resolution
Analyse Crystal structure of udp-N-acetylglucosamine pyrophosphorylase (AGX2) from mus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VM8
- Type
- protein
- Length
- 981 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
- Q91YN5
- Ligands
- CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) | protein | 491 | 36% helix, 23% strand | Q91YN5 |
| B | Udp-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) | protein | 490 | 38% helix, 22% strand | Q91YN5 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.85 | 135 | empty |
| 2 | 281 | 0.69 | 0.84 | 39 | empty |
| 3 | 151 | 0.60 | 0.83 | 33 | empty |
| 4 | 473 | 0.58 | 0.74 | 47 | empty |
| 5 | 314 | 0.55 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1446 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 1VM8 · Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q91YN5 · AlphaFold monomer V2.0 prediction for udp-N-acetylhexosamine pyrophosphorylase (Q91YN5) · a predicted model of the same protein · chain B 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 Q91YN5
- Elsewhere: RCSB PDB 1VM8 · PDBe 1VM8 · UniProt Q91YN5
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