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Crystal structure of L-fuconate dehydratase from xanthomonas campestris pv. campestris str. atcc 33913
Analyse Crystal structure of L-fuconate dehydratase from xanthomonas campestris pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YEY
- Type
- protein
- Length
- 1,725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-fuconate dehydratase
- UniProt
- Q8P3K2
- Ligands
- MG
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-fuconate dehydratase | protein | 425 | 47% helix, 15% strand | Q8P3K2 |
| B | L-fuconate dehydratase | protein | 432 | 46% helix, 16% strand | Q8P3K2 |
| C | L-fuconate dehydratase | protein | 435 | 47% helix, 15% strand | Q8P3K2 |
| D | L-fuconate dehydratase | protein | 433 | 46% helix, 15% strand | Q8P3K2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.72 | 0.97 | 30 | MG |
| 2 | 54 | 0.72 | 0.99 | 23 | empty |
| 3 | 57 | 0.71 | 0.98 | 23 | empty |
| 4 | 532 | 0.64 | 0.76 | 69 | empty |
| 5 | 292 | 0.60 | 0.79 | 45 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2543 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2526 Ų buried · 58 hydrogen bonds · protein-protein
- B–D · 347 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1YEY · Crystal Structure of L-fuconate Dehydratase from Xanthomonas campestris pv. campestris… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8P3K2 · AlphaFold monomer V2.0 prediction for L-fuconate dehydratase (Q8P3K2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8P3K2
- Elsewhere: RCSB PDB 1YEY · PDBe 1YEY · UniProt Q8P3K2
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