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Crystal structure of L-fuconate dehydratase from silicibacter sp. TM1040 liganded with mg and D-erythronohydroxamate
Analyse Crystal structure of L-fuconate dehydratase from silicibacter sp. TM1040… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IP5
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein
- UniProt
- Q1GLV3
- Ligands
- EHM, MG
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein | protein | 421 | 46% helix, 16% strand | Q1GLV3 |
Ligands and binding sites
- EHM · (2R,3R)-N,2,3,4-tetrahydroxybutanamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.33 | 0.76 | 16 | empty |
| 2 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2512 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 4IP5 · Crystal structure of l-fuconate dehydratase from Silicibacter sp. tm1040 liganded with Mg… · 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 Q1GLV3
- Elsewhere: RCSB PDB 4IP5 · PDBe 4IP5 · UniProt Q1GLV3
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