Research workbench
Mouse semaphorin 3A, domains sema-psi-ig
Analyse Mouse semaphorin 3A, domains sema-psi-ig in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZ8
- Type
- protein
- Length
- 1,112 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-3A
- UniProt
- O08665
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin-3A | protein | 557 | 7% helix, 38% strand | O08665 |
| B | Semaphorin-3A | protein | 555 | 7% helix, 38% strand | O08665 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.84 | 0.84 | 79 | empty |
| 2 | 971 | 0.74 | 0.78 | 87 | CA |
| 3 | 901 | 0.74 | 0.78 | 82 | CA |
| 4 | 204 | 0.56 | 0.79 | 31 | empty |
| 5 | 242 | 0.54 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1243 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 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 O08665
- Elsewhere: RCSB PDB 4GZ8 · PDBe 4GZ8 · UniProt O08665
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