Research workbench
Structure of the recombinant lectin pvl from psathyrella velutina in complex with glcnacb-D-1,3GALACTOSIDE
Analyse Structure of the recombinant lectin pvl from psathyrella velutina in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UP4
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin pvl
- UniProt
- Q309D1
- Ligands
- NAG, GAL, NDG, CA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin pvl | protein | 400 | 3% helix, 37% strand | Q309D1 |
| B | Lectin pvl | protein | 399 | 3% helix, 37% strand | Q309D1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.82 | 0.83 | 67 | empty |
| 2 | 1005 | 0.81 | 0.82 | 67 | empty |
| 3 | 260 | 0.63 | 0.81 | 33 | empty |
| 4 | 230 | 0.63 | 0.82 | 31 | empty |
| 5 | 208 | 0.60 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4UP4 · Structure of the recombinant lectin PVL from Psathyrella velutina in complex with… · 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 Q309D1
- Elsewhere: RCSB PDB 4UP4 · PDBe 4UP4 · UniProt Q309D1
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