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Crystal structure of 1,3GAL43A, an exo-beta-1,3-galactanase from clostridium thermocellum
Analyse Crystal structure of 1,3GAL43A, an exo-beta-1,3-galactanase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VSF
- Type
- protein
- Length
- 2,787 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin B lectin
- UniProt
- A3DD67
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Ricin B lectin | protein | 461 | 6% helix, 49% strand | A3DD67 |
| C | Ricin B lectin | protein | 482 | 6% helix, 46% strand | A3DD67 |
Ligands and binding sites
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.78 | 0.80 | 98 | GOL |
| 2 | 769 | 0.77 | 0.81 | 91 | GOL |
| 3 | 301 | 0.67 | 0.82 | 38 | empty |
| 4 | 295 | 0.64 | 0.81 | 48 | empty |
| 5 | 576 | 0.62 | 0.74 | 55 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1116 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 705 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 656 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 633 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3VSF · Crystal structure of 1,3Gal43A, an exo-beta-1,3-Galactanase from Clostridium thermocellum · 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 A3DD67
- Elsewhere: RCSB PDB 3VSF · PDBe 3VSF · UniProt A3DD67
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