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Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from aureobasidium namibiae (ANGH128_VI) with laminaribiose at the surface-binding site
Analyse Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UBB
- Type
- protein
- Length
- 2,472 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYCO_HYDRO_CC domain-containing protein
- UniProt
- A0A074W9U7
- Ligands
- BGC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H, I, J | GLYCO_HYDRO_CC domain-containing protein | protein | 247 | 40% helix, 18% strand | A0A074W9U7 |
| C | GLYCO_HYDRO_CC domain-containing protein | protein | 249 | 40% helix, 18% strand | A0A074W9U7 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D, E, F, G, H, I, J
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 | 1124 | 0.81 | 0.82 | 111 | empty |
| 2 | 1136 | 0.81 | 0.82 | 108 | empty |
| 3 | 631 | 0.78 | 0.84 | 64 | empty |
| 4 | 334 | 0.63 | 0.79 | 41 | empty |
| 5 | 269 | 0.63 | 0.81 | 42 | empty |
Interfaces
19 interfaces between chains.
- I–J · 1111 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1082 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 1067 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 1058 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 1043 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6UBB · Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium… · 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 A0A074W9U7
- Elsewhere: RCSB PDB 6UBB · PDBe 6UBB · UniProt A0A074W9U7
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