Research workbench
Crystal structure of a lectin from canavalia gladiata seeds (cgl) in complex with MAN1-4MAN-ome
Analyse Crystal structure of a lectin from canavalia gladiata seeds (cgl) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P2K
- Type
- protein
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Canavalia gladiata lectin
- UniProt
- P14894
- Ligands
- MMA, MAN, MN, CA
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Canavalia gladiata lectin | protein | 234 | 4% helix, 45% strand | P14894 |
| B, D | Canavalia gladiata lectin | protein | 234 | 4% helix, 46% strand | P14894 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.85 | 0.87 | 113 | empty |
| 2 | 61 | 0.47 | 0.85 | 16 | empty |
| 3 | 56 | 0.34 | 0.78 | 22 | empty |
| 4 | 60 | 0.31 | 0.76 | 24 | empty |
| 5 | 65 | 0.30 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1087 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1071 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 893 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 855 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2P2K · Crystal structure of a lectin from Canavalia gladiata seeds (CGL) in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P14894 · AlphaFold monomer V2.0 prediction for concanavalin-a (P14894) · a predicted model of the same protein · chain C against A, TM-score 0.51
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 P14894
- Elsewhere: RCSB PDB 2P2K · PDBe 2P2K · UniProt P14894
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