MolNFT v1 · #82518 · protein
Crystal structure of a 2-fluoroxylotriosyl complex of the vibrio sp. ax-4 beta-1,3-xylanase
3VPL · Beta-1,3-xylanase XYL4: “Crystal structure of a 2-fluoroxylotriosyl complex of the vibrio sp. ax-4 beta-1,3-xylanase”. X-ray diffraction, 3 ligands (BXF, DNX, XYP), 1 pocket (best druggability 0.66). MolNFT v1 #82518 on GenesisL1…
- PDB
- 3VPL
- Type
- protein
- Length
- 324 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,3-xylanase XYL4
- EC
- 3.2.1.32
- UniProt
- D5MP61
- Ligands
- BXF, DNX, XYP
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,3-xylanase XYL4 (EC 3.2.1.32) | protein | 324 | 37% helix, 19% strand | D5MP61 |
Ligands and binding sites
- BXF · 2-deoxy-2-fluoro-beta-D-xylopyranose · ligand · 2 copies · chains A
- DNX · 3,4-dinitrophenol · ligand · chains A
- XYP · beta-D-xylopyranose · sugar · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.66 | 0.80 | 42 | BXF, XYP, DNX |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 3VPL · Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4… · the same entry in another collection · chain A against A, TM-score 1.00
- D5MP61 · AlphaFold monomer V2.0 prediction for beta-1,3-xylanase XYL4 (D5MP61) · a predicted model of the same protein · 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 D5MP61
- Elsewhere: RCSB PDB 3VPL · PDBe 3VPL · UniProt D5MP61
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