MolNFT v1 · #153426 · protein
Ligand complex structure of GH10 family xylanase XYNAF1, soaking for 40 minutes
6JE1 · Beta-xylanase: “Ligand complex structure of GH10 family xylanase XYNAF1, soaking for 40 minutes”. X-ray diffraction, 2 ligands (XYP, NAG), 2 pockets (best druggability 0.47). MolNFT v1 #153426 on GenesisL1: 3D structure, binding…
- PDB
- 6JE1
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- A0A0J5Q413
- Ligands
- XYP, NAG
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 319 | 42% helix, 20% strand | A0A0J5Q413 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
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 | 149 | 0.47 | 0.77 | 33 | XYP, GOL |
| 2 | 119 | 0.44 | 0.77 | 27 | XYP, GOL |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6JE1 · Ligand complex structure of GH10 family xylanase XynAF1, soaking for 40 minutes · 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 A0A0J5Q413
- Elsewhere: RCSB PDB 6JE1 · PDBe 6JE1 · UniProt A0A0J5Q413
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