MolNFT v1 · #127498 · protein
Homodimerization of TIE2 fibronectin-like domains 2 and 3 in space group P21
5MYB · Angiopoietin-1 receptor: “Homodimerization of TIE2 fibronectin-like domains 2 and 3 in space group P21”. X-ray diffraction, 2 ligands (NAG, BMA), 2 pockets (best druggability 0.54). MolNFT v1 #127498 on GenesisL1: 3D structure…
- PDB
- 5MYB
- Type
- protein
- Length
- 381 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
- Pockets
- 2 · best druggability 0.54
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 | 190 | 0% helix, 46% strand | Q02763 |
| B | Angiopoietin-1 receptor (EC 2.7.10.1) | protein | 191 | 0% helix, 46% strand | Q02763 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-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 | 141 | 0.54 | 0.81 | 21 | empty |
| 2 | 93 | 0.50 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 5MYB · Homodimerization of Tie2 Fibronectin-like domains 2 and 3 in space group P21 · the same entry in another collection · chain B against B, TM-score 1.00
- Q02763 · AlphaFold monomer V2.0 prediction for angiopoietin-1 receptor (Q02763) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 5MYB · PDBe 5MYB · UniProt Q02763
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