Research workbench
Plexin A2 in complex with semaphorin 6A
Analyse Plexin A2 in complex with semaphorin 6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OKY
- Type
- protein
- Length
- 1,149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A2; Putative uncharacterized protein
- UniProt
- P70207, Q8BUT0
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-A2 | protein | 609 | 9% helix, 40% strand | P70207 |
| B | Putative uncharacterized protein | protein | 540 | 11% helix, 38% strand | Q8BUT0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.82 | 0.83 | 90 | empty |
| 2 | 968 | 0.78 | 0.80 | 64 | GOL |
| 3 | 891 | 0.76 | 0.79 | 80 | GOL |
| 4 | 281 | 0.62 | 0.80 | 49 | empty |
| 5 | 115 | 0.48 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1132 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 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 P70207
- Every structure of UniProt Q8BUT0
- Elsewhere: RCSB PDB 3OKY · PDBe 3OKY · UniProt P70207 · UniProt Q8BUT0
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