Research workbench
Crystal structure of CT1,3GAL43A in complex with lactose
Analyse Crystal structure of CT1,3GAL43A in complex with lactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VT0
- 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
- BGC, GAL
- Pockets
- 20 · best druggability 0.77
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
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, E, F
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, E, F
- GOL · Glycerol · additive · 3 copies · chains A, C, 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 | 182 | 0.77 | 0.93 | 36 | GOL |
| 2 | 718 | 0.76 | 0.82 | 82 | empty |
| 3 | 749 | 0.69 | 0.76 | 77 | empty |
| 4 | 60 | 0.64 | 0.93 | 19 | empty |
| 5 | 301 | 0.62 | 0.79 | 45 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1114 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 730 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 661 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 650 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 637 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VT0 · Crystal structure of Ct1,3Gal43A in complex with lactose · 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 3VT0 · PDBe 3VT0 · UniProt A3DD67
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