Research workbench
Rmlc P aeruginosa with dtdp-4-keto rhamnnose (the product of the reaction)
Analyse Rmlc P aeruginosa with dtdp-4-keto rhamnnose (the product of the reaction) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IXK
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose 3,5-epimerase
- UniProt
- Q9HU21
- Ligands
- TDO
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-4-dehydrorhamnose 3,5-epimerase | protein | 184 | 10% helix, 46% strand | Q9HU21 |
Ligands and binding sites
- TDO · Dtdp-4-keto-L-rhamnose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.75 | 0.98 | 22 | empty |
| 2 | 220 | 0.67 | 0.85 | 27 | TDO |
| 3 | 230 | 0.66 | 0.84 | 32 | TDO |
| 4 | 89 | 0.55 | 0.85 | 17 | empty |
| 5 | 82 | 0.49 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1625 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2IXK · RmlC P aeruginosa with dTDP-4-keto rhamnnose (the product of the reaction) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HU21 · AlphaFold monomer V2.0 prediction for dtdp-4-dehydrorhamnose 3,5-epimerase (Q9HU21) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9HU21
- Elsewhere: RCSB PDB 2IXK · PDBe 2IXK · UniProt Q9HU21
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