MolNFT v1 · #33829 · protein
Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent sialoglycopeptide from glycophorin a
2CWG · Agglutinin isolectin 1 (WGA1): “Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent…”. X-ray diffraction, 3 ligands (SIA, NDG, GAL), 5 pockets (best druggability 0.63). MolNFT…
- PDB
- 2CWG
- Type
- protein
- Length
- 353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin isolectin 1 (WGA1); T5 sialoglycopeptide of glycophorin a
- UniProt
- P10968
- Ligands
- SIA, NDG, GAL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Agglutinin isolectin 1 (WGA1) | protein | 171 | 23% helix, 20% strand | P10968 |
| D | T5 sialoglycopeptide of glycophorin a | protein | 8 | 0% helix, 0% strand | — |
| E | T5 sialoglycopeptide of glycophorin a | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains D, A, B, E
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains D, B, E
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.63 | 0.91 | 19 | empty |
| 2 | 75 | 0.62 | 0.91 | 20 | empty |
| 3 | 71 | 0.58 | 0.89 | 26 | empty |
| 4 | 97 | 0.40 | 0.76 | 20 | SIA |
| 5 | 58 | 0.27 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2400 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 116 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 104 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 2 modified, 1 glycan (disulfide, cyclization, O-glycosylation).
Compared structures
- 2CWG · Crystallographic refinement and structure analysis of the complex of wheat germ… · the same entry in another collection · chain B against B, TM-score 1.00
- P10968 · AlphaFold monomer V2.0 prediction for agglutinin isolectin 1 (P10968) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P10968
- Elsewhere: RCSB PDB 2CWG · PDBe 2CWG · UniProt P10968
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