MolNFT v1 · #119982 · protein
Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase from a compostmicrobial metagenome, calcium-bound form
5GLL · Glycoside hydrolase family 43: “Crystal structure of COXYL43, GH43 beta-XYLOSIDASE/ALPHA- arabinofuranosidase from a compostmicrobial…”. X-ray diffraction, 2 ligands (CA, NA), 5 pockets (best druggability 0.73). MolNFT v1 #119982 on…
- PDB
- 5GLL
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 43
- UniProt
- A0A0H5BL38
- Ligands
- CA, NA
- Pockets
- 5 · best druggability 0.73
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 | 331 | 4% helix, 42% strand | A0A0H5BL38 |
| B | Glycoside hydrolase family 43 | protein | 325 | 4% helix, 42% strand | A0A0H5BL38 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.73 | 0.93 | 28 | GOL, ACT |
| 2 | 121 | 0.70 | 0.91 | 29 | GOL, ACT |
| 3 | 805 | 0.70 | 0.76 | 72 | NA |
| 4 | 213 | 0.56 | 0.79 | 23 | empty |
| 5 | 219 | 0.55 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5GLL · 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 5GLL · PDBe 5GLL · UniProt A0A0H5BL38
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