Research workbench
Crystal structure of streptomyces rapamycinicus GH74 in complex with xyloglucan fragments xllg and xxxg
Analyse Crystal structure of streptomyces rapamycinicus GH74 in complex with xyloglucan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P2O
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucanase
- UniProt
- A0A0A0NH71
- Ligands
- BGC, XYS, GAL, SO4, CL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xyloglucanase | protein | 727 | 3% helix, 38% strand | A0A0A0NH71 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 16 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 12 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.84 | 0.94 | 35 | empty |
| 2 | 386 | 0.83 | 0.92 | 37 | empty |
| 3 | 846 | 0.74 | 0.78 | 123 | BGC, XYS |
| 4 | 299 | 0.73 | 0.86 | 54 | empty |
| 5 | 391 | 0.61 | 0.77 | 62 | BGC, XYS |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6P2O · Crystal structure of Streptomyces rapamycinicus GH74 in complex with xyloglucan fragments… · 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 A0A0A0NH71
- Elsewhere: RCSB PDB 6P2O · PDBe 6P2O · UniProt A0A0A0NH71
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