MolNFT v1 · #82634 · protein
Crystal structure of CT1,3GAL43A in complex with galactose
3VT1 · Ricin B lectin: “Crystal structure of CT1,3GAL43A in complex with galactose”. X-ray diffraction, 1 ligand (GAL), 20 pockets (best druggability 0.77). MolNFT v1 #82634 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VT1
- 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 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, E, F, A | Ricin B lectin | protein | 461 | 5% helix, 50% strand | A3DD67 |
| C | Ricin B lectin | protein | 482 | 6% helix, 46% strand | A3DD67 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 7 copies · chains B, C, E, F, A
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 | 726 | 0.77 | 0.82 | 88 | empty |
| 2 | 465 | 0.75 | 0.84 | 61 | empty |
| 3 | 796 | 0.69 | 0.76 | 73 | empty |
| 4 | 65 | 0.65 | 0.93 | 18 | empty |
| 5 | 524 | 0.64 | 0.76 | 43 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1149 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 705 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 665 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 658 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VT1 · Crystal structure of Ct1,3Gal43A in complex with galactose · the same entry in another collection · chain B against B, 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 3VT1 · PDBe 3VT1 · UniProt A3DD67
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.