MolNFT v1 · #83262 · protein
Crystal structure of plant lectin (ligand-free form)
3WCR · Erythroagglutinin: “Crystal structure of plant lectin (ligand-free form)”. X-ray diffraction, 2 ligands (NAG, BR), 3 pockets (best druggability 0.65). MolNFT v1 #83262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WCR
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythroagglutinin
- UniProt
- V5YN37
- Ligands
- NAG, BR
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythroagglutinin | protein | 229 | 5% helix, 49% strand | V5YN37 |
| B | Erythroagglutinin | protein | 235 | 7% helix, 49% strand | V5YN37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BR · Bromide ion · ion · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.65 | 0.80 | 49 | BR |
| 2 | 278 | 0.65 | 0.82 | 42 | BR |
| 3 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 3WCR · Crystal structure of plant lectin (ligand-free form) · 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 V5YN37
- Elsewhere: RCSB PDB 3WCR · PDBe 3WCR · UniProt V5YN37
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