MolNFT v1 · #164311 · protein
Three dimensional structure of the giant reed (arundodonax) lectin (adl) complex with N,N'-diacetylchitobiose; 60 seconds soaking
6STR · Arundo donax lectin (adl): “Three dimensional structure of the giant reed (arundodonax) lectin (adl) complex with…”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.61). MolNFT v1 #164311 on GenesisL1: 3D…
- PDB
- 6STR
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arundo donax lectin (adl)
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Arundo donax lectin (adl) | protein | 165 | 24% helix, 20% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.61 | 0.87 | 31 | NAG |
| 2 | 131 | 0.60 | 0.85 | 35 | NAG |
| 3 | 74 | 0.39 | 0.79 | 24 | empty |
| 4 | 69 | 0.35 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2240 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
- 6STR · Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with… · 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 6STR · PDBe 6STR
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