MolNFT v1 · #125307 · protein
Plexin A1 full extracellular region, domains 1 to 10, to 6 ångström, spacegroup P2(1)
5L59 · Plexin-A1: “Plexin A1 full extracellular region, domains 1 to 10, to 6 ångström, spacegroup P2(1)”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #125307 on GenesisL1: 3D structure…
- PDB
- 5L59
- Type
- protein
- Length
- 2,342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A1
- UniProt
- P70206
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plexin-A1 | protein | 1171 | 7% helix, 39% strand | P70206 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 31 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 16 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.76 | 0.79 | 63 | empty |
| 2 | 891 | 0.76 | 0.79 | 64 | empty |
| 3 | 506 | 0.73 | 0.82 | 49 | empty |
| 4 | 50 | 0.46 | 0.85 | 15 | empty |
| 5 | 157 | 0.43 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 5L59 · Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P2(1) · the same entry in another collection · chain A against A, TM-score 1.00
- P70206 · AlphaFold monomer V2.0 prediction for plexin-A1 (P70206) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P70206
- Elsewhere: RCSB PDB 5L59 · PDBe 5L59 · UniProt P70206
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