MolNFT v1 · #82632 · protein
Crystal structure of CT1,3GAL43A in complex with galactan
3VSZ · Ricin B lectin: “Crystal structure of CT1,3GAL43A in complex with galactan”. X-ray diffraction, 1 ligand (GAL), 20 pockets (best druggability 0.79). MolNFT v1 #82632 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VSZ
- 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
- Ligands
- GAL
- Pockets
- 20 · best druggability 0.79
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
- GAL · beta-D-galactopyranose · sugar · 17 copies · chains A, B, C, E, F
- GOL · Glycerol · additive · 10 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.79 | 0.94 | 33 | GOL |
| 2 | 809 | 0.77 | 0.81 | 96 | GAL, GOL |
| 3 | 779 | 0.70 | 0.76 | 68 | empty |
| 4 | 722 | 0.68 | 0.76 | 62 | empty |
| 5 | 59 | 0.67 | 0.96 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1122 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 663 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 651 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 616 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VSZ · Crystal structure of Ct1,3Gal43A in complex with galactan · 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 3VSZ · PDBe 3VSZ · UniProt A3DD67
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