MolNFT v1 · #142560 · protein
Pholiota squarrosa lectin
6A86: “Pholiota squarrosa lectin”. X-ray diffraction, 1 ligand (BU4), 4 pockets (best druggability 0.53). MolNFT v1 #142560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A86
- Type
- protein
- Length
- 237 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- BU4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Lectin | protein | 40 | 0% helix, 65% strand | — |
| D | Lectin | protein | 39 | 0% helix, 67% strand | — |
| F | Lectin | protein | 38 | 0% helix, 66% strand | — |
Ligands and binding sites
- BU4 · (3R)-butane-1,3-diol · ligand · 4 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.53 | 0.82 | 15 | BU4 |
| 2 | 105 | 0.36 | 0.74 | 13 | empty |
| 3 | 79 | 0.33 | 0.75 | 20 | empty |
| 4 | 54 | 0.28 | 0.75 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–C · 673 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 668 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 665 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 664 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 649 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6A86 · Pholiota squarrosa lectin · 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 6A86 · PDBe 6A86
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