MolNFT v1 · #16386 · protein
Crystal structure of mnmn concanavalin a
1NXD: “Crystal structure of mnmn concanavalin a”. X-ray diffraction, 3 ligands (MN, NA, AZI), 2 pockets (best druggability 0.60). MolNFT v1 #16386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NXD
- 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
- MN, NA, AZI
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4 | Concanavalin a | protein | 237 | 5% helix, 46% strand | P02866 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains 1, 2, 3, 4
- NA · Sodium ion · metal · 4 copies · chains 1, 2, 3, 4
- AZI · Azide ion · ion · 16 copies · chains 1, 2, 3, 4
- GOL · Glycerol · additive · 25 copies · chains 1, 2, 3, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.60 | 0.79 | 27 | AZI, GOL |
| 2 | 92 | 0.40 | 0.77 | 17 | GOL |
Interfaces
2 interfaces between chains.
- 1–2 · 1237 Ų buried · 22 hydrogen bonds · protein-protein
- 3–4 · 411 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 1NXD · PDBe 1NXD · UniProt P02866
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