Research workbench
Mouse semaphorin 6A, extracellular domains 1-2
Analyse Mouse semaphorin 6A, extracellular domains 1-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OKW
- Type
- protein
- Length
- 1,062 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-6A
- UniProt
- O35464
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin-6A | protein | 540 | 11% helix, 39% strand | O35464 |
| B | Semaphorin-6A | protein | 522 | 9% helix, 37% strand | O35464 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 10 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.78 | 0.80 | 67 | GOL |
| 2 | 1068 | 0.77 | 0.79 | 75 | GOL |
| 3 | 854 | 0.77 | 0.80 | 74 | empty |
| 4 | 129 | 0.46 | 0.78 | 26 | empty |
| 5 | 84 | 0.44 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
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 O35464
- Elsewhere: RCSB PDB 3OKW · PDBe 3OKW · UniProt O35464
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