Research workbench
Structure of the semaphorin 3A receptor-binding module
Analyse Structure of the semaphorin 3A receptor-binding module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q47
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin 3A
- UniProt
- O08665
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin 3A | protein | 484 | 8% helix, 39% strand | O08665 |
| B | Semaphorin 3A | protein | 495 | 7% helix, 42% strand | O08665 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.84 | 0.85 | 88 | empty |
| 2 | 984 | 0.74 | 0.77 | 82 | empty |
| 3 | 914 | 0.74 | 0.78 | 94 | empty |
| 4 | 129 | 0.48 | 0.78 | 20 | empty |
| 5 | 115 | 0.42 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1478 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation, 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 1Q47 · PDBe 1Q47 · UniProt O08665
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