Research workbench
Crystal structure of sll-2
Analyse Crystal structure of sll-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WMP
- Type
- protein
- Length
- 564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-binding lectin
- UniProt
- A4CYJ6
- Ligands
- NAG, A2G, GLA, NA, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Galactose-binding lectin | protein | 94 | 0% helix, 60% strand | A4CYJ6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, F, E
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains B, C
- GLA · alpha-D-galactopyranose · sugar · chains D, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.99 | 21 | empty |
| 2 | 74 | 0.75 | 0.98 | 21 | empty |
| 3 | 54 | 0.69 | 0.97 | 18 | empty |
| 4 | 50 | 0.68 | 0.97 | 18 | empty |
| 5 | 57 | 0.36 | 0.79 | 21 | empty |
Interfaces
15 interfaces between chains.
- D–F · 902 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 893 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 892 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 885 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3WMP · Crystal structure of SLL-2 · 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 3WMP · PDBe 3WMP · UniProt A4CYJ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.