MolNFT v1 · #148589 · protein
Teneurin 2 partial extracellular domain
6FB3 · Teneurin-2: “Teneurin 2 partial extracellular domain”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #148589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FB3
- Type
- protein
- Length
- 7,344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Teneurin-2
- UniProt
- Q9DER5
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Teneurin-2 | protein | 1836 | 7% helix, 47% strand | Q9DER5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 68 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, B, D, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
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 | 824 | 0.87 | 0.90 | 92 | empty |
| 2 | 746 | 0.87 | 0.90 | 79 | empty |
| 3 | 425 | 0.86 | 0.94 | 69 | empty |
| 4 | 774 | 0.86 | 0.90 | 87 | empty |
| 5 | 744 | 0.86 | 0.90 | 88 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1070 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1068 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
- 6FB3 · Teneurin 2 Partial Extracellular Domain · the same entry in another collection · chain A against A, 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 Q9DER5
- Elsewhere: RCSB PDB 6FB3 · PDBe 6FB3 · UniProt Q9DER5
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