MolNFT v1 · #1559 · protein
Native cardosin a from cynara cardunculus L.
1B5F · Protein (cardosin a): “Native cardosin a from cynara cardunculus L.”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 5 pockets (best druggability 0.78). MolNFT v1 #1559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1B5F
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cardosin a)
- EC
- 3.4.23.-
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (cardosin a) (EC 3.4.23.-) | protein | 239 | 13% helix, 47% strand | — |
| B, D | Protein (cardosin a) (EC 3.4.23.-) | protein | 87 | 16% helix, 48% strand | — |
| C | Protein (cardosin a) (EC 3.4.23.-) | protein | 238 | 13% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.78 | 0.80 | 87 | empty |
| 2 | 392 | 0.61 | 0.76 | 41 | empty |
| 3 | 322 | 0.58 | 0.76 | 43 | empty |
| 4 | 151 | 0.47 | 0.77 | 26 | empty |
| 5 | 65 | 0.37 | 0.78 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3208 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3113 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1B5F · Native cardosin a from cynara cardunculus L. · the same entry in another collection · chain A against A, 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 1B5F · PDBe 1B5F
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