MolNFT v1 · #156829 · protein
Crystal structure of the catalytic domain from GH74 enzyme POGH74 from paenibacillus odorifer, in complex with xlx xyloglucan
6MGK · Xyloglucanase: “Crystal structure of the catalytic domain from GH74 enzyme POGH74 from paenibacillus odorifer, in complex…”. X-ray diffraction, 4 ligands (BGC, XYS, GAL), 20 pockets (best druggability 0.83). MolNFT v1 #156829 on…
- 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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