Research workbench
Crystal structure of pholiota squarrosa lectin in complex with an octasaccharide
Analyse Crystal structure of pholiota squarrosa lectin in complex with an octasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FX1
- Type
- protein
- Length
- 487 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- C4W, OOA, NAG, MAN, BMA, FUC
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 6 distinct chains · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, H, J | Lectin | protein | 40 | 0% helix, 65% strand | — |
| B, E | Lectin | protein | 42 | 0% helix, 62% strand | — |
| D, K | Lectin | protein | 39 | 0% helix, 64% strand | — |
| F | Lectin | protein | 41 | 0% helix, 61% strand | — |
| I | Lectin | protein | 43 | 0% helix, 58% strand | — |
| L | Lectin | protein | 41 | 0% helix, 61% strand | — |
Ligands and binding sites
- C4W · 1-azido-beta-N-acetyl-D-glucosamine · ligand · 12 copies · chains B, C, A, G, I, E, F, D, J, L, H, K
- OOA · 3-oxooctanoic acid · ligand · chains A, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, G, I, D, E, F, J, H, K, L
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B, C, E, F, G, L
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G
- FUC · alpha-L-fucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MLI · Malonate ion · additive · 12 copies · chains A, C, B, D, F, E, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.55 | 0.80 | 26 | empty |
| 2 | 200 | 0.54 | 0.78 | 24 | empty |
| 3 | 226 | 0.54 | 0.77 | 25 | OOA |
| 4 | 158 | 0.44 | 0.75 | 26 | C4W, FUC |
| 5 | 134 | 0.43 | 0.76 | 22 | C4W, FUC |
Interfaces
31 interfaces between chains.
- H–I · 735 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 719 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 713 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 707 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 702 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6FX1 · Crystal structure of Pholiota squarrosa lectin in complex with an octasaccharide · 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 6FX1 · PDBe 6FX1
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