Research workbench
Crystal structure of the mutant Y90F of divergent galactarate dehydratase from oceanobacillus iheyensis complexed with mg and galactarate
Analyse Crystal structure of the mutant Y90F of divergent galactarate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPF
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase
- UniProt
- Q8EMJ9
- Ligands
- GAE, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Muconate cycloisomerase | protein | 387 | 40% helix, 20% strand | Q8EMJ9 |
Ligands and binding sites
- GAE · D-galactaric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.74 | 0.82 | 56 | GAE |
| 2 | 494 | 0.73 | 0.82 | 62 | GAE |
| 3 | 73 | 0.48 | 0.83 | 21 | empty |
| 4 | 72 | 0.48 | 0.83 | 20 | empty |
| 5 | 76 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1351 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3HPF · Crystal structure of the mutant Y90F of divergent galactarate dehydratase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EMJ9 · AlphaFold monomer V2.0 prediction for galactarate dehydratase (D-threo-forming) (Q8EMJ9) · 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 Q8EMJ9
- Elsewhere: RCSB PDB 3HPF · PDBe 3HPF · UniProt Q8EMJ9
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