MolNFT v1 · #156828 · protein
Crystal structure of the catalytic domain from GH74 enzyme POGH74 from paenibacillus odorifer, apoenzyme
6MGJ · Xyloglucanase: “Crystal structure of the catalytic domain from GH74 enzyme POGH74 from paenibacillus odorifer, apoenzyme”. X-ray diffraction, 3 ligands (MG, PO4, CL), 20 pockets (best druggability 0.83). MolNFT v1 #156828 on…
- PDB
- 6MGJ
- Type
- protein
- Length
- 5,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucanase
- UniProt
- A0A1R0YRH0
- Ligands
- MG, PO4, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Xyloglucanase | protein | 747 | 3% helix, 37% strand | A0A1R0YRH0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · chains D
- CL · Chloride ion · ion · chains F
- GOL · Glycerol · additive · 36 copies · chains A, B, C, D, E, F, G, H
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.83 | 0.85 | 94 | empty |
| 2 | 896 | 0.82 | 0.85 | 95 | empty |
| 3 | 873 | 0.82 | 0.85 | 88 | empty |
| 4 | 494 | 0.80 | 0.87 | 48 | MG |
| 5 | 666 | 0.80 | 0.84 | 81 | empty |
Interfaces
11 interfaces between chains.
- C–H · 845 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 775 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 665 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 638 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 144 modified (engineered).
Compared structures
- 6MGJ · 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 6MGJ · PDBe 6MGJ · UniProt A0A1R0YRH0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.