MolNFT v1 · #17246 · protein
Co-crystals of concanavalin a with methyl-3,6-di-O-(alpha-D- mannopyranosyl)-alpha-D-mannopyranoside
1ONA: “Co-crystals of concanavalin a with methyl-3,6-di-O-(alpha-D- mannopyranosyl)-alpha-D-mannopyranoside”. X-ray diffraction, 4 ligands (MAN, MMA, MN), 3 pockets (best druggability 0.86). MolNFT v1 #17246 on GenesisL1: 3D structure…
- PDB
- 1ONA
- Type
- protein
- Length
- 924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin a
- UniProt
- P02866
- Ligands
- MAN, MMA, MN, CA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Concanavalin a | protein | 231 | 4% helix, 44% strand | P02866 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, D, B
- CA · Calcium ion · metal · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.86 | 0.87 | 105 | empty |
| 2 | 75 | 0.42 | 0.80 | 21 | empty |
| 3 | 52 | 0.31 | 0.76 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1049 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1049 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1ONA · Co-crystals of concanavalin a with methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannop… · the same entry in another collection · chain D against D, TM-score 1.00
- P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain B 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 P02866
- Elsewhere: RCSB PDB 1ONA · PDBe 1ONA · UniProt P02866
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