Research workbench
Banana lectin bound to xyl-B1,3 man-a-O-methyl (xm)
Analyse Banana lectin bound to xyl-B1,3 man-a-O-methyl (xm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BMZ
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ripening-associated protein
- UniProt
- O22321
- Ligands
- MMA, XYP, CD, SO4
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 68% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ripening-associated protein | protein | 141 | 0% helix, 70% strand | O22321 |
| B | Ripening-associated protein | protein | 138 | 0% helix, 67% strand | O22321 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.31 | 0.75 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 347 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2BMZ · Banana Lectin bound to Xyl-b1,3 Man-a-O-Methyl (XM) · 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 O22321
- Elsewhere: RCSB PDB 2BMZ · PDBe 2BMZ · UniProt O22321
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