MolNFT v1 · #189892 · protein
Crystal structure of TXGH116 E730Q mutant from thermoanaerobacterium xylanolyticum with glucose
7W2T · Glucosylceramidase: “Crystal structure of TXGH116 E730Q mutant from thermoanaerobacterium xylanolyticum with glucose”. X-ray diffraction, 2 ligands (BGC, CA), 11 pockets (best druggability 0.57). MolNFT v1 #189892 on GenesisL1: 3D…
- PDB
- 7W2T
- Type
- protein
- Length
- 1,544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- F6BL85
- Ligands
- BGC, CA
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 773 | 31% helix, 22% strand | F6BL85 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 771 | 31% helix, 23% strand | F6BL85 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.57 | 0.74 | 42 | GOL |
| 2 | 277 | 0.55 | 0.76 | 34 | empty |
| 3 | 111 | 0.53 | 0.83 | 26 | BGC, GOL |
| 4 | 255 | 0.53 | 0.76 | 38 | empty |
| 5 | 139 | 0.52 | 0.80 | 25 | BGC, GOL |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7W2T · Crystal structure of TxGH116 E730Q 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 7W2T · PDBe 7W2T · UniProt F6BL85
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