Research workbench
Crystal structure of exo-GLUCOSIDASE/GLUCOSAMINIDASE VC0615 from vibrio cholerae
Analyse Crystal structure of exo-GLUCOSIDASE/GLUCOSAMINIDASE VC0615 from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GDT
- Type
- protein
- Length
- 2,826 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase-related protein
- UniProt
- Q9KUA8
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endoglucanase-related protein | protein | 566 | 39% helix, 18% strand | Q9KUA8 |
| E | Endoglucanase-related protein | protein | 562 | 40% helix, 18% strand | Q9KUA8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.84 | 0.92 | 53 | empty |
| 2 | 1180 | 0.80 | 0.81 | 92 | empty |
| 3 | 772 | 0.74 | 0.79 | 70 | empty |
| 4 | 198 | 0.67 | 0.85 | 25 | empty |
| 5 | 204 | 0.67 | 0.85 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1013 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 769 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 417 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GDT · Crystal structure of exo-glucosidase/glucosaminidase VC0615 from Vibrio Cholerae · 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 Q9KUA8
- Elsewhere: RCSB PDB 6GDT · PDBe 6GDT · UniProt Q9KUA8
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