MolNFT v1 · #125314 · protein
Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 ångström
5L5G · Plexin-A2: “Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 ångström”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #125314 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L5G
- Type
- protein
- Length
- 3,701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A2
- UniProt
- P70207
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-A2 | protein | 906 | 9% helix, 40% strand | P70207 |
| B | Plexin-A2 | protein | 809 | 10% helix, 39% strand | P70207 |
| C, D | Plexin-A2 | protein | 993 | 8% helix, 40% strand | P70207 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.77 | 0.84 | 62 | empty |
| 2 | 959 | 0.76 | 0.79 | 89 | empty |
| 3 | 965 | 0.76 | 0.78 | 90 | empty |
| 4 | 584 | 0.71 | 0.79 | 45 | empty |
| 5 | 573 | 0.70 | 0.79 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 655 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 640 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 disulfide (disulfide).
Compared structures
- 5L5G · Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
- P70207 · AlphaFold monomer V2.0 prediction for plexin-A2 (P70207) · a predicted model of the same protein · chain C 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 P70207
- Elsewhere: RCSB PDB 5L5G · PDBe 5L5G · UniProt P70207
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