Research workbench
Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium and L-tartrate
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
- 4HCH
- 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
- MG, NA
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ISOMERASE/LACTONIZING enzyme | protein | 384 | 38% helix, 23% strand | Q7CSI0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.85 | 0.92 | 74 | PGE, TLA, GOL |
| 2 | 81 | 0.65 | 0.92 | 24 | GOL |
| 3 | 59 | 0.60 | 0.92 | 18 | empty |
| 4 | 64 | 0.38 | 0.79 | 14 | empty |
| 5 | 53 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4HCH · 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 4HCH · PDBe 4HCH · UniProt Q7CSI0
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