Research workbench
The endo-BETA1,6-glucanase BT3312
Analyse The endo-BETA1,6-glucanase BT3312 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGL
- Type
- protein
- Length
- 1,356 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- UniProt
- A0A173SYZ2
- Ligands
- NOJ, BGC, NA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase | protein | 450 | 30% helix, 28% strand | A0A173SYZ2 |
| B | Glucosylceramidase | protein | 454 | 30% helix, 28% strand | A0A173SYZ2 |
| C | Glucosylceramidase | protein | 452 | 30% helix, 29% strand | A0A173SYZ2 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 3 copies · chains A, B, C
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.71 | 0.77 | 80 | empty |
| 2 | 720 | 0.69 | 0.76 | 66 | empty |
| 3 | 442 | 0.64 | 0.77 | 56 | empty |
| 4 | 99 | 0.38 | 0.76 | 19 | NOJ, BGC |
| 5 | 94 | 0.38 | 0.76 | 19 | NOJ, BGC |
Interfaces
3 interfaces between chains.
- A–C · 507 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 405 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5NGL · The endo-beta1,6-glucanase BT3312 · 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 A0A173SYZ2
- Elsewhere: RCSB PDB 5NGL · PDBe 5NGL · UniProt A0A173SYZ2
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