Research workbench
Crystal structure of L-rhamnonate dehydratase from salmonella typhimurium
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
- 2P3Z
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-rhamnonate dehydratase
- EC
- 4.2.1.90
- UniProt
- Q8ZNF9
- Ligands
- NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-rhamnonate dehydratase (EC 4.2.1.90) | protein | 405 | 38% helix, 17% strand | Q8ZNF9 |
| B | L-rhamnonate dehydratase (EC 4.2.1.90) | protein | 405 | 35% helix, 17% strand | Q8ZNF9 |
Ligands and binding sites
- NA · Sodium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.74 | 0.97 | 29 | empty |
| 2 | 51 | 0.71 | 0.99 | 18 | empty |
| 3 | 181 | 0.55 | 0.80 | 31 | empty |
| 4 | 206 | 0.54 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2399 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2P3Z · Crystal structure of L-Rhamnonate dehydratase from Salmonella typhimurium · 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 B 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 2P3Z · PDBe 2P3Z · UniProt Q8ZNF9
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