MolNFT v1 · #115555 · protein
Refined structure of concanavalin a complexed with alpha-methyl-D- mannopyranoside at 2.0 ångströms resolution and comparison with the saccharide-free structure
5CNA: “Refined structure of concanavalin a complexed with alpha-methyl-D- mannopyranoside at 2.0 ångströms…”. X-ray diffraction, 4 ligands (MMA, MN, CA), 9 pockets (best druggability 0.82). MolNFT v1 #115555 on GenesisL1: 3D structure…
- PDB
- 5CNA
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin a
- UniProt
- P02866
- Ligands
- MMA, MN, CA, CL
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Concanavalin a | protein | 237 | 4% helix, 47% strand | P02866 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · 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
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.82 | 0.92 | 68 | empty |
| 2 | 312 | 0.80 | 0.91 | 60 | empty |
| 3 | 147 | 0.74 | 0.93 | 33 | empty |
| 4 | 64 | 0.70 | 0.97 | 22 | empty |
| 5 | 89 | 0.62 | 0.89 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1207 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1201 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1189 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1171 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CNA · Refined structure of concanavalin a complexed with alpha-methyl-D-mannopyranoside at 2.0… · 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 D against A, TM-score 0.50
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 5CNA · PDBe 5CNA · UniProt P02866
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