MolNFT v1 · #164011 · protein
Teneurin 2 in complex with latrophilin 2 lec domain
6SKE · Teneurin-2: “Teneurin 2 in complex with latrophilin 2 lec domain”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #164011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SKE
- Type
- protein
- Length
- 3,696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Teneurin-2; Adhesion G protein-coupled receptor L2
- UniProt
- Q9DER5, Q8JZZ7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Teneurin-2 | protein | 1752 | 7% helix, 46% strand | Q9DER5 |
| B, D | Adhesion G protein-coupled receptor L2 | protein | 96 | 15% helix, 39% strand | Q8JZZ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1021 | 0.87 | 0.88 | 88 | empty |
| 2 | 1090 | 0.87 | 0.88 | 96 | empty |
| 3 | 1032 | 0.87 | 0.88 | 92 | empty |
| 4 | 1136 | 0.87 | 0.88 | 99 | empty |
| 5 | 968 | 0.84 | 0.85 | 114 | empty |
Interfaces
3 interfaces between chains.
- B–C · 811 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 802 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 657 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 6SKE · Teneurin 2 in complex with Latrophilin 2 Lec domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q8JZZ7 · AlphaFold monomer V2.0 prediction for adhesion G protein-coupled receptor L2 (Q8JZZ7) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9DER5
- Every structure of UniProt Q8JZZ7
- Elsewhere: RCSB PDB 6SKE · PDBe 6SKE · UniProt Q9DER5 · UniProt Q8JZZ7
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