MolNFT v1 · #119065 · 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
5FKT · Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, GLY74A: “Unraveling the first step of xyloglucan degradation by the soil saprophyte cellvibrio japonicus through the…”. X-ray diffraction, 2 ligands (K, BR), 10 pockets (best druggability…
- PDB
- 5FKT
- Type
- protein
- Length
- 1,464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, GLY74A
- EC
- 3.2.1.-, 3.2.1.151
- UniProt
- B3PKK9
- Ligands
- K, BR
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, GLY74A (EC 3.2.1.-, 3.2.1.151) | protein | 731 | 2% helix, 38% strand | B3PKK9 |
| B | Endo-1,4-beta-GLUCANASE/XYLOGLUCANASE, GLY74A (EC 3.2.1.-, 3.2.1.151) | protein | 733 | 2% helix, 39% strand | B3PKK9 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.83 | 0.90 | 47 | empty |
| 2 | 479 | 0.81 | 0.88 | 48 | empty |
| 3 | 952 | 0.76 | 0.79 | 91 | EDO |
| 4 | 243 | 0.74 | 0.88 | 40 | empty |
| 5 | 236 | 0.73 | 0.88 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 325 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FKT · 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 5FKT · PDBe 5FKT · UniProt B3PKK9
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