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Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium and L-lyxarohydroxamate
Analyse Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HCL
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ISOMERASE/LACTONIZING enzyme
- UniProt
- Q7CSI0
- Ligands
- LLH, MG
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ISOMERASE/LACTONIZING enzyme | protein | 384 | 39% helix, 23% strand | Q7CSI0 |
Ligands and binding sites
- LLH · (2R,3S,4R)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.88 | 0.90 | 114 | LLH, PG4 |
| 2 | 301 | 0.77 | 0.89 | 51 | LLH |
| 3 | 66 | 0.39 | 0.79 | 14 | empty |
| 4 | 56 | 0.37 | 0.80 | 13 | empty |
| 5 | 60 | 0.36 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1725 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4HCL · CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed… · 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 Q7CSI0
- Elsewhere: RCSB PDB 4HCL · PDBe 4HCL · UniProt Q7CSI0
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