Research workbench
Crystal structure of the mutant P34A of D-glucarate dehydratase from escherichia COLI complexed with product 5-keto-4-deoxy-D-glucarate
Analyse Crystal structure of the mutant P34A of D-glucarate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PWI
- Type
- protein
- Length
- 881 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- UniProt
- E2KTD9
- Ligands
- GLR, MG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucarate dehydratase | protein | 440 | 40% helix, 18% strand | E2KTD9 |
| B | Glucarate dehydratase | protein | 441 | 39% helix, 17% strand | E2KTD9 |
Ligands and binding sites
- GLR · 2,3-dihydroxy-5-oxo-hexanedioate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.68 | 0.85 | 33 | empty |
| 2 | 238 | 0.66 | 0.84 | 36 | empty |
| 3 | 120 | 0.46 | 0.79 | 19 | empty |
| 4 | 154 | 0.44 | 0.75 | 29 | empty |
| 5 | 93 | 0.44 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 146 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3PWI · Crystal structure of the mutant P34A of D-Glucarate dehydratase from Escherichia coli… · the same entry in another collection · 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 E2KTD9
- Elsewhere: RCSB PDB 3PWI · PDBe 3PWI · UniProt E2KTD9
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