Research workbench
Plexin A1 full extracellular region, domains 1 to 10, to 6 ångström, spacegroup P4(3)2(1)2
Analyse Plexin A1 full extracellular region, domains 1 to 10, to 6 ångström, spacegroup… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L5C
- Type
- protein
- Length
- 1,171 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A1
- UniProt
- P70206
- Ligands
- NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-A1 | protein | 1171 | 7% helix, 39% strand | P70206 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 7 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.76 | 0.80 | 65 | empty |
| 2 | 60 | 0.53 | 0.87 | 18 | empty |
| 3 | 121 | 0.40 | 0.75 | 20 | empty |
| 4 | 112 | 0.38 | 0.75 | 24 | empty |
| 5 | 58 | 0.33 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 24 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5L5C · Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P4(3)2(1)2 · 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 0.77
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 5L5C · PDBe 5L5C · UniProt P70206
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