Research workbench
Crystal structure of the GH74 xyloglucanase from xanthomonas campestris (XCC1752)
Analyse Crystal structure of the GH74 xyloglucanase from xanthomonas campestris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KN8
- Type
- protein
- Length
- 1,415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase
- UniProt
- Q8P9U5
- Ligands
- BGC, XYS, NA, IOD
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulase | protein | 707 | 4% helix, 40% strand | Q8P9U5 |
| B | Cellulase | protein | 708 | 4% helix, 40% strand | Q8P9U5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 14 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.83 | 0.94 | 46 | EDO, NA |
| 2 | 226 | 0.83 | 0.96 | 36 | EDO, NA |
| 3 | 688 | 0.81 | 0.85 | 48 | empty |
| 4 | 663 | 0.80 | 0.85 | 46 | EDO |
| 5 | 884 | 0.73 | 0.77 | 65 | BGC, XYS, EDO, IOD |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KN8 · Crystal structure of the GH74 xyloglucanase from Xanthomonas campestris (Xcc1752) · 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 Q8P9U5
- Elsewhere: RCSB PDB 7KN8 · PDBe 7KN8 · UniProt Q8P9U5
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