Research workbench
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
Analyse Unraveling the first step of xyloglucan degradation by the soil saprophyte… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FKR
- 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
- K, BR
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 38% 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 | 2% helix, 38% strand | B3PKK9 |
Ligands and binding sites
- K · Potassium ion · metal · 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 | 447 | 0.82 | 0.89 | 43 | empty |
| 2 | 169 | 0.64 | 0.85 | 32 | empty |
| 3 | 414 | 0.60 | 0.76 | 57 | empty |
| 4 | 205 | 0.45 | 0.74 | 27 | empty |
| 5 | 132 | 0.42 | 0.75 | 23 | EDO |
Compared structures
- 5FKR · 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 5FKR · PDBe 5FKR · UniProt B3PKK9
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