MolNFT v1 · #62605 · protein
Crystal structure of L-rhamnonate dehydratase from azotobacter vinelandii complexed with mg and L-tartrate
3EKG · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of L-rhamnonate dehydratase from azotobacter vinelandii complexed with mg and L-tartrate”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.72).…
- PDB
- 3EKG
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q4J3N3
- Ligands
- MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 395 | 38% helix, 17% strand | Q4J3N3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.72 | 0.98 | 22 | TLA |
| 2 | 57 | 0.71 | 0.98 | 20 | TLA |
| 3 | 169 | 0.51 | 0.78 | 36 | empty |
| 4 | 163 | 0.45 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2466 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3EKG · CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with… · the same entry in another collection · chain B against B, 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 Q4J3N3
- Elsewhere: RCSB PDB 3EKG · PDBe 3EKG · UniProt Q4J3N3
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