Research workbench
GH5 endo-xyloglucanase from cellvibrio japonicus
Analyse GH5 endo-xyloglucanase from cellvibrio japonicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OYC
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase, putative, CEL5D
- EC
- 3.2.1.151
- UniProt
- B3PD52
- Ligands
- SO4, CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 373 | 40% helix, 14% strand | B3PD52 |
| B | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 371 | 40% helix, 15% strand | B3PD52 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 20 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · chains A, B
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 | 262 | 0.56 | 0.77 | 37 | GOL, SO4 |
| 2 | 215 | 0.52 | 0.77 | 27 | empty |
| 3 | 114 | 0.50 | 0.81 | 19 | PG4 |
| 4 | 238 | 0.49 | 0.75 | 26 | GOL |
| 5 | 140 | 0.48 | 0.78 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 751 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5OYC · GH5 endo-xyloglucanase from Cellvibrio japonicus · 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 B3PD52
- Elsewhere: RCSB PDB 5OYC · PDBe 5OYC · UniProt B3PD52
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