Research workbench
Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase from a compostmicrobial metagenome in complex with xylotriose, calcium-bound form
Analyse Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GLN
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 43
- UniProt
- A0A0H5BL38
- Ligands
- XYP, XYS, CA, NA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 43 | protein | 330 | 4% helix, 42% strand | A0A0H5BL38 |
| B | Glycoside hydrolase family 43 | protein | 325 | 4% helix, 42% strand | A0A0H5BL38 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 11 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.71 | 0.92 | 26 | XYP, XYS |
| 2 | 163 | 0.68 | 0.88 | 32 | XYP, XYS |
| 3 | 712 | 0.67 | 0.75 | 73 | XYP, NA, ACT |
| 4 | 210 | 0.56 | 0.79 | 23 | empty |
| 5 | 217 | 0.56 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5GLN · Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a… · 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 A0A0H5BL38
- Elsewhere: RCSB PDB 5GLN · PDBe 5GLN · UniProt A0A0H5BL38
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