MolNFT v1 · #119064 · protein
Unraveling the first step of xyloglucan degradation by the soil saprophyte cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase
5FKS · Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, putative, GLY74A: “Unraveling the first step of xyloglucan degradation by the soil saprophyte cellvibrio japonicus through the…”. X-ray diffraction, 5 ligands (BGC, XYS, GAL), 6 pockets (best…
- PDB
- 5FKS
- Type
- protein
- Length
- 731 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, putative, GLY74A
- EC
- 3.2.1.-, 3.2.1.151
- UniProt
- B3PKK9
- Ligands
- BGC, XYS, GAL, K, BR
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, putative, GLY74A (EC 3.2.1.-, 3.2.1.151) | protein | 731 | 3% helix, 39% strand | B3PKK9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A
- XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A
- BR · Bromide ion · ion · chains A
- EDO · 1,2-ethanediol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.81 | 0.89 | 45 | K |
| 2 | 209 | 0.72 | 0.88 | 39 | empty |
| 3 | 409 | 0.60 | 0.76 | 58 | BGC, XYS, GAL |
| 4 | 186 | 0.45 | 0.74 | 29 | empty |
| 5 | 128 | 0.43 | 0.76 | 20 | EDO |
Compared structures
- 5FKS · Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio… · 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 B3PKK9
- Elsewhere: RCSB PDB 5FKS · PDBe 5FKS · UniProt B3PKK9
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