MolNFT v1 · #2414 · protein
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase
1BVV · Endo-1,4-beta-xylanase: “Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase”. X-ray diffraction, 2 ligands (DFX, XYP), 1 pocket (best druggability 0.49). MolNFT v1 #2414 on GenesisL1: 3D structure…
- PDB
- 1BVV
- Type
- protein
- Length
- 185 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- P09850
- Ligands
- DFX, XYP
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 185 | 5% helix, 61% strand | P09850 |
Ligands and binding sites
- DFX · 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol · ligand · chains A
- XYP · beta-D-xylopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.49 | 0.78 | 27 | DFX, XYP |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1BVV · Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase · the same entry in another collection · chain A against A, TM-score 1.00
- P09850 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P09850) · a predicted model of the same protein · chain A 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 P09850
- Elsewhere: RCSB PDB 1BVV · PDBe 1BVV · UniProt P09850
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