Research workbench
Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium, L-xylarohydroxamate 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
- 4MMW
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ISOMERASE/LACTONIZING enzyme
- UniProt
- Q7CSI0
- Ligands
- XYH, LLH, MG, CL
- Pockets
- 8 · 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 | 381 | 39% helix, 23% strand | Q7CSI0 |
Ligands and binding sites
- XYH · Xylarohydroxamate · ligand · 2 copies · chains A, B
- LLH · (2R,3S,4R)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 10 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.88 | 0.90 | 106 | XYH, LLH, PGE |
| 2 | 271 | 0.76 | 0.89 | 53 | XYH, LLH |
| 3 | 82 | 0.41 | 0.78 | 14 | empty |
| 4 | 64 | 0.36 | 0.77 | 14 | empty |
| 5 | 68 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1699 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4MMW · Crystal structure of D-glucarate dehydratase from Agrobacterium tumefaciens complexed… · the same entry in another collection · chain B against B, 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 4MMW · PDBe 4MMW · UniProt Q7CSI0
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