Research workbench
Plexin A2 / semaphorin 6A complex
Analyse Plexin A2 / semaphorin 6A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AL8
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-6A; Plexin-A2
- UniProt
- O35464, P70207
- Ligands
- NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin-6A | protein | 537 | 9% helix, 37% strand | O35464 |
| B | Plexin-A2 | protein | 499 | 10% helix, 40% strand | P70207 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.84 | 0.88 | 58 | empty |
| 2 | 941 | 0.78 | 0.80 | 68 | empty |
| 3 | 881 | 0.74 | 0.78 | 75 | empty |
| 4 | 553 | 0.67 | 0.77 | 64 | empty |
| 5 | 77 | 0.51 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1222 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3AL8 · Plexin A2 / Semaphorin 6A complex · the same entry in another collection · chain A against A, TM-score 1.00
- O35464 · AlphaFold monomer V2.0 prediction for semaphorin-6A (O35464) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P70207 · AlphaFold monomer V2.0 prediction for plexin-A2 (P70207) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Every structure of UniProt P70207
- Elsewhere: RCSB PDB 3AL8 · PDBe 3AL8 · UniProt O35464 · UniProt P70207
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