MolNFT v1 · #127497 · protein
Homodimerization of TIE2 fibronectin-like domains 1-3 in space group C2
5MYA · Angiopoietin-1 receptor: “Homodimerization of TIE2 fibronectin-like domains 1-3 in space group C2”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 2 pockets (best druggability 0.55). MolNFT v1 #127497 on GenesisL1: 3D structure…
- PDB
- 5MYA
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiopoietin-1 receptor
- EC
- 2.7.10.1
- UniProt
- Q02763
- Ligands
- NAG, BMA, MAN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiopoietin-1 receptor (EC 2.7.10.1) | protein | 292 | 0% helix, 46% strand | Q02763 |
| B | Angiopoietin-1 receptor (EC 2.7.10.1) | protein | 191 | 0% helix, 45% strand | Q02763 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.55 | 0.81 | 25 | empty |
| 2 | 137 | 0.50 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 755 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 5MYA · Homodimerization of Tie2 Fibronectin-like domains 1-3 in space group C2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q02763 · AlphaFold monomer V2.0 prediction for angiopoietin-1 receptor (Q02763) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q02763
- Elsewhere: RCSB PDB 5MYA · PDBe 5MYA · UniProt Q02763
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