MolNFT v1 · #136854 · protein
Complex of NLGN2 with MDGA1 IG1-IG2
5V5V · Neuroligin-2: “Complex of NLGN2 with MDGA1 IG1-IG2”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #136854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V5V
- Type
- protein
- Length
- 4,266 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin-2; Mam domain-containing glycosylphosphatidylinositol anchor protein 1
- UniProt
- Q62888, Q8NFP4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Neuroligin-2 | protein | 527 | 36% helix, 13% strand | Q62888 |
| G, H, I, J, K, L | Mam domain-containing glycosylphosphatidylinositol anchor protein 1 | protein | 184 | 3% helix, 49% strand | Q8NFP4 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.74 | 0.77 | 87 | empty |
| 2 | 447 | 0.69 | 0.80 | 63 | empty |
| 3 | 453 | 0.67 | 0.79 | 49 | empty |
| 4 | 473 | 0.66 | 0.78 | 54 | empty |
| 5 | 500 | 0.65 | 0.77 | 60 | empty |
Interfaces
20 interfaces between chains.
- F–J · 878 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 867 Ų buried · 8 hydrogen bonds · protein-protein
- D–K · 863 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 863 Ų buried · 2 hydrogen bonds · protein-protein
- C–L · 854 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 5V5V · Complex of NLGN2 with MDGA1 Ig1-Ig2 · the same entry in another collection · chain L against L, TM-score 1.00
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 Q62888
- Every structure of UniProt Q8NFP4
- Elsewhere: RCSB PDB 5V5V · PDBe 5V5V · UniProt Q62888 · UniProt Q8NFP4
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