Research workbench
Crystal structure of an antiflamatory legume lectin from cymbosema roseum seeds
Analyse Crystal structure of an antiflamatory legume lectin from cymbosema roseum seeds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A0K
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cymbosema roseum mannose-specific lectin
- Ligands
- ABA, MN, CA
- Pockets
- 1 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cymbosema roseum mannose-specific lectin | protein | 232 | 4% helix, 46% strand | — |
| E, G | Cymbosema roseum mannose-specific lectin | protein | 237 | 4% helix, 45% strand | — |
Ligands and binding sites
- ABA · Alpha-aminobutyric acid · ligand · 2 copies · chains E, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
- CA · Calcium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.85 | 0.86 | 126 | empty |
Interfaces
4 interfaces between chains.
- E–G · 1173 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1067 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1011 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 922 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3A0K · Crystal structure of an antiflamatory legume lectin from Cymbosema roseum seeds · the same entry in another collection · chain G against G, 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
- Elsewhere: RCSB PDB 3A0K · PDBe 3A0K
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