MolNFT v1 · #189894 · protein
Crystal structure of TXGH116 R786K mutant from thermoanaerobacterium xylanolyticum with glucose
7W2W · Glucosylceramidase: “Crystal structure of TXGH116 R786K mutant from thermoanaerobacterium xylanolyticum with glucose”. X-ray diffraction, 4 ligands (GLC, BGC, CA), 5 pockets (best druggability 0.63). MolNFT v1 #189894 on GenesisL1…
- PDB
- 7W2W
- Type
- protein
- Length
- 771 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- F6BL85
- Ligands
- GLC, BGC, CA, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 771 | 31% helix, 23% strand | F6BL85 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 12 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.63 | 0.81 | 29 | GLC, BGC, GOL |
| 2 | 128 | 0.44 | 0.76 | 22 | empty |
| 3 | 67 | 0.36 | 0.77 | 13 | GOL |
| 4 | 61 | 0.32 | 0.76 | 18 | empty |
| 5 | 55 | 0.28 | 0.74 | 18 | empty |
Compared structures
- 7W2W · Crystal structure of TxGH116 R786K mutant from Thermoanaerobacterium xylanolyticum with… · 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 F6BL85
- Elsewhere: RCSB PDB 7W2W · PDBe 7W2W · UniProt F6BL85
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