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Crystal structure of L-rhamnonate dehydratase from salmonella typhimurium complexed with mg and D-malate
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
- 3D47
- Type
- protein
- Length
- 3,240 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative galactonate dehydratase
- UniProt
- Q8ZNF9
- Ligands
- MLT, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative galactonate dehydratase | protein | 405 | 38% helix, 17% strand | Q8ZNF9 |
Ligands and binding sites
- MLT · D-malate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.88 | 0.90 | 103 | empty |
| 2 | 880 | 0.88 | 0.90 | 106 | empty |
| 3 | 965 | 0.87 | 0.89 | 107 | empty |
| 4 | 636 | 0.86 | 0.90 | 88 | empty |
| 5 | 598 | 0.84 | 0.89 | 68 | empty |
Interfaces
16 interfaces between chains.
- C–D · 2386 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2378 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2376 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2370 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2104 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3D47 · Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with… · the same entry in another collection · chain H against H, 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 3D47 · PDBe 3D47 · UniProt Q8ZNF9
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