MolNFT v1 · #61139 · protein
Lecb (pa-lii) in complex with the synthetic ligand 2G0
3DCQ · Fucose-binding lectin pa-iil: “Lecb (pa-lii) in complex with the synthetic ligand 2G0”. X-ray diffraction, 2 ligands (2G0, CA), 2 pockets (best druggability 0.33). MolNFT v1 #61139 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DCQ
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin pa-iil
- UniProt
- Q9HYN5
- Ligands
- 2G0, CA
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin pa-iil | protein | 114 | 0% helix, 71% strand | Q9HYN5 |
Ligands and binding sites
- 2G0 · (2S)-1-[(2S)-6-amino-2-({[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl]acetyl}amino)hexanoyl]-N-[(1S)-1-carbamoyl-3-methylbutyl]pyrrolidine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.33 | 0.73 | 19 | empty |
| 2 | 94 | 0.32 | 0.73 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1333 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 522 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3DCQ · LECB (PA-LII) in complex with the synthetic ligand 2G0 · 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
- Every structure of UniProt Q9HYN5
- Elsewhere: RCSB PDB 3DCQ · PDBe 3DCQ · UniProt Q9HYN5
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