Research workbench
Crystal structure of pha-E lectin in complex with bisected glycan
Analyse Crystal structure of pha-E lectin in complex with bisected glycan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AVA
- Type
- protein
- Length
- 1,904 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythroagglutinin
- UniProt
- V5YN37
- Ligands
- NAG, MAN, BMA, GAL, MN, CA
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Erythroagglutinin | protein | 238 | 5% helix, 46% strand | V5YN37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.71 | 0.79 | 75 | empty |
| 2 | 708 | 0.71 | 0.78 | 68 | empty |
| 3 | 647 | 0.71 | 0.79 | 62 | empty |
| 4 | 583 | 0.69 | 0.79 | 61 | empty |
| 5 | 408 | 0.56 | 0.74 | 50 | empty |
Interfaces
11 interfaces between chains.
- G–H · 924 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 916 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 910 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 886 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 728 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5AVA · Crystal structure of PHA-E lectin in complex with bisected glycan · 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 5AVA · PDBe 5AVA · UniProt V5YN37
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