Research workbench
Crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from aquifex aeolicus VF5
Analyse Crystal structure of udp-N-acetylglucosamine 1-carboxyvinyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YVW
- Type
- protein
- Length
- 416 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 1-carboxyvinyltransferase
- EC
- 2.5.1.7
- UniProt
- O67315
- Ligands
- EPU, PO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) | protein | 416 | 34% helix, 28% strand | O67315 |
Ligands and binding sites
- EPU · Uridine-diphosphate-2(N-acetylglucosaminyl) butyric acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.79 | 0.85 | 62 | PO4, EPU |
| 2 | 59 | 0.26 | 0.72 | 19 | empty |
Compared structures
- 2YVW · Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67315 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · a predicted model of the same protein · 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 O67315
- Elsewhere: RCSB PDB 2YVW · PDBe 2YVW · UniProt O67315
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