MolNFT v1 · #48305 · protein
Crystal structure of L-TALARATE/GALACTARATE dehydratase mutant K197A liganded with mg and L-glucarate
2PP3: “Crystal structure of L-TALARATE/GALACTARATE dehydratase mutant K197A liganded with mg and L-glucarate”. X-ray diffraction, 2 ligands (LGT, MG), 7 pockets (best druggability 0.81). MolNFT v1 #48305 on GenesisL1: 3D structure, binding…
- PDB
- 2PP3
- Type
- protein
- Length
- 1,185 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-TALARATE/GALACTARATE dehydratase
- UniProt
- Q8ZL58
- Ligands
- LGT, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-TALARATE/GALACTARATE dehydratase | protein | 395 | 39% helix, 21% strand | Q8ZL58 |
Ligands and binding sites
- LGT · L-glucaric acid · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.81 | 0.82 | 68 | empty |
| 2 | 1176 | 0.78 | 0.80 | 100 | empty |
| 3 | 161 | 0.65 | 0.86 | 35 | LGT |
| 4 | 156 | 0.63 | 0.85 | 34 | MG, LGT |
| 5 | 159 | 0.63 | 0.85 | 34 | MG, LGT |
Interfaces
3 interfaces between chains.
- B–C · 3069 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 81 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2PP3 · Crystal structure of L-talarate/galactarate dehydratase mutant K197A liganded with Mg and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZL58 · AlphaFold monomer V2.0 prediction for L-TALARATE/GALACTARATE dehydratase (Q8ZL58) · a predicted model of the same protein · chain A against A, 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 Q8ZL58
- Elsewhere: RCSB PDB 2PP3 · PDBe 2PP3 · UniProt Q8ZL58
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