Research workbench
Pholiota squarrosa lectin (phosl) in complex with FUCOSE(ALPHA1-6) glcnac
Analyse Pholiota squarrosa lectin (phosl) in complex with FUCOSE(ALPHA1-6) glcnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A87
- Type
- protein
- Length
- 238 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- MEE, FUC, NAG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Lectin | protein | 40 | 0% helix, 65% strand | — |
| D, F | Lectin | protein | 39 | 0% helix, 64% strand | — |
Ligands and binding sites
- MEE · Methanethiol · ligand · 3 copies · chains E, F
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains D, F, E, A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, F, E
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 | 111 | 0.58 | 0.84 | 17 | empty |
| 2 | 174 | 0.45 | 0.74 | 37 | empty |
Interfaces
9 interfaces between chains.
- A–C · 679 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 671 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 667 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 664 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6A87 · Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)GlcNAc · 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 6A87 · PDBe 6A87
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