MolNFT v1 · #78897 · protein
Crystal structure of putative L-alanine-dl-glutamate epimerase from burkholderia xenovorans strain LB400 bound to magnesium and alpha- ketoglutarate
3SN4: “Crystal structure of putative L-alanine-dl-glutamate epimerase from burkholderia xenovorans strain LB400…”. X-ray diffraction, 4 ligands (AKG, MG, NA), 3 pockets (best druggability 0.60). MolNFT v1 #78897 on GenesisL1: 3D structure…
- PDB
- 3SN4
- Type
- protein
- Length
- 396 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative L-alanine-dl-glutamate epimerase
- UniProt
- Q13PB7
- Ligands
- AKG, MG, NA, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative L-alanine-dl-glutamate epimerase | protein | 396 | 41% helix, 19% strand | Q13PB7 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.60 | 0.85 | 31 | AKG |
| 2 | 60 | 0.52 | 0.87 | 25 | empty |
| 3 | 108 | 0.45 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3SN4 · Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia… · 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 Q13PB7
- Elsewhere: RCSB PDB 3SN4 · PDBe 3SN4 · UniProt Q13PB7
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