Research workbench
Crystal structure of the catalytic domain from GH74 enzyme POGH74 from paenibacillus odorifer, in complex with xlx xyloglucan
Analyse Crystal structure of the catalytic domain from GH74 enzyme POGH74 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MGK
- Type
- protein
- Length
- 2,988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucanase
- UniProt
- A0A1R0YRH0
- Ligands
- BGC, XYS, GAL, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xyloglucanase | protein | 747 | 3% helix, 38% strand | A0A1R0YRH0 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D
- XYS · alpha-D-xylopyranose · sugar · 9 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 45 copies · chains A, D, C, B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.83 | 0.85 | 91 | GOL |
| 2 | 867 | 0.83 | 0.85 | 91 | GOL |
| 3 | 512 | 0.81 | 0.88 | 60 | CL |
| 4 | 550 | 0.81 | 0.87 | 51 | empty |
| 5 | 619 | 0.81 | 0.86 | 60 | GOL |
Interfaces
6 interfaces between chains.
- A–D · 801 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 460 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 6MGK · Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus… · 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 A0A1R0YRH0
- Elsewhere: RCSB PDB 6MGK · PDBe 6MGK · UniProt A0A1R0YRH0
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