MolNFT v1 · #119986 · protein
Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase from a compostmicrobial metagenome in complex with L-arabinose, calcium-bound form
5GLP · Glycoside hydrolase family 43: “Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase from a compostmicrobial…”. X-ray diffraction, 3 ligands (ARA, CA, NA), 6 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 5GLP
- 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
- ARA, CA, NA
- Pockets
- 6 · best druggability 0.74
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
- ARA · alpha-L-arabinopyranose · sugar · 4 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 · chains A
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 | 115 | 0.74 | 0.94 | 25 | ARA |
| 2 | 113 | 0.72 | 0.93 | 26 | ARA |
| 3 | 814 | 0.69 | 0.76 | 78 | NA |
| 4 | 203 | 0.56 | 0.79 | 24 | empty |
| 5 | 223 | 0.55 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5GLP · 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 5GLP · PDBe 5GLP · UniProt A0A0H5BL38
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.