MolNFT v1 · #139081 · protein
Sll-2-forssman antigen tetrasaccharides complex
5X4A · Galactose-binding lectin: “Sll-2-forssman antigen tetrasaccharides complex”. X-ray diffraction, 5 ligands (NAG, GLA, GAL), 13 pockets (best druggability 0.76). MolNFT v1 #139081 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5X4A
- Type
- protein
- Length
- 1,128 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-binding lectin
- UniProt
- A4CYJ6
- Ligands
- NAG, GLA, GAL, NGA, A2G
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Galactose-binding lectin | protein | 94 | 0% helix, 64% strand | A4CYJ6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GLA · alpha-D-galactopyranose · sugar · 11 copies · chains H, I, A, C
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains F, H, I, K
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.99 | 21 | empty |
| 2 | 60 | 0.74 | 0.99 | 21 | empty |
| 3 | 57 | 0.70 | 0.97 | 18 | empty |
| 4 | 50 | 0.70 | 0.98 | 18 | empty |
| 5 | 51 | 0.69 | 0.98 | 18 | empty |
Interfaces
31 interfaces between chains.
- H–I · 915 Ų buried · 16 hydrogen bonds · protein-protein
- J–L · 910 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 906 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 903 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5X4A · SLL-2-Forssman antigen tetrasaccharides complex · 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 A4CYJ6
- Elsewhere: RCSB PDB 5X4A · PDBe 5X4A · UniProt A4CYJ6
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