Research workbench
Crystal structure of L-rhamnonate dehydratase from salmonella typhimurium complexed with mg and 3-deoxy-L- rhamnonate
Analyse Crystal structure of L-rhamnonate dehydratase from salmonella typhimurium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CXO
- Type
- protein
- Length
- 804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative galactonate dehydratase
- UniProt
- Q8ZNF9
- Ligands
- 3LR, 1N5, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative galactonate dehydratase | protein | 402 | 37% helix, 17% strand | Q8ZNF9 |
Ligands and binding sites
- 3LR · 3,6-dideoxy-L-arabino-hexonic acid · ligand · chains A
- 1N5 · (2R,4S)-2,4,7-trihydroxyheptanoic acid · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.76 | 0.97 | 30 | empty |
| 2 | 53 | 0.70 | 0.98 | 19 | 1N5 |
| 3 | 53 | 0.70 | 0.98 | 20 | 3LR |
| 4 | 191 | 0.55 | 0.79 | 31 | empty |
| 5 | 188 | 0.53 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2381 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3CXO · Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZNF9 · AlphaFold monomer V2.0 prediction for L-rhamnonate dehydratase (Q8ZNF9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8ZNF9
- Elsewhere: RCSB PDB 3CXO · PDBe 3CXO · UniProt Q8ZNF9
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