MolNFT v1 · #84864 · protein
Engineering the active site of a GH43 glycoside hydrolase generates a biotechnologically significant enzyme that displays both endo- xylanase and exo-arabinofuranosidase activity
3ZXK · HIAXHD3: “Engineering the active site of a GH43 glycoside hydrolase generates a biotechnologically significant enzyme…”. X-ray diffraction, 2 ligands (XYP, AHR), 10 pockets (best druggability 0.66). MolNFT v1 #84864 on GenesisL1: 3D…
- PDB
- 3ZXK
- Type
- protein
- Length
- 1,059 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIAXHD3
- EC
- 3.2.1.55
- Ligands
- XYP, AHR
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIAXHD3 (EC 3.2.1.55) | protein | 530 | 4% helix, 47% strand | — |
| B | HIAXHD3 (EC 3.2.1.55) | protein | 529 | 3% helix, 48% strand | — |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, B
- AHR · alpha-L-arabinofuranose · sugar · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.66 | 0.74 | 68 | empty |
| 2 | 279 | 0.58 | 0.78 | 31 | empty |
| 3 | 117 | 0.57 | 0.84 | 20 | XYP, AHR |
| 4 | 202 | 0.56 | 0.79 | 22 | empty |
| 5 | 201 | 0.55 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 139 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3ZXK · Engineering the active site of a GH43 glycoside hydrolase generates a biotechnologically… · 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
- Elsewhere: RCSB PDB 3ZXK · PDBe 3ZXK
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