MolNFT v1 · #147531 · protein
Crystal structure of DPR2 IG1-IG2 in complex with dip-theta IG1-IG3
6EG1 · Defective proboscis extension response 2, isoform F: “Crystal structure of DPR2 IG1-IG2 in complex with dip-theta IG1-IG3”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 2 pockets (best druggability 0.38). MolNFT v1 #147531 on…
- PDB
- 6EG1
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Defective proboscis extension response 2, isoform F; Dpr-interacting protein theta
- UniProt
- Q59DZ4, Q9VMN6
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Defective proboscis extension response 2, isoform F | protein | 220 | 3% helix, 50% strand | Q59DZ4 |
| B, D | Dpr-interacting protein theta | protein | 295 | 3% helix, 58% strand | Q9VMN6 |
| C | Defective proboscis extension response 2, isoform F | protein | 219 | 3% helix, 50% strand | Q59DZ4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 10 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FLC · Citrate anion · additive · 2 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
- BU3 · (R,R)-2,3-butanediol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.38 | 0.80 | 14 | empty |
| 2 | 50 | 0.36 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 965 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 6EG1 · Crystal structure of Dpr2 Ig1-Ig2 in complex with DIP-Theta Ig1-Ig3 · 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 Q59DZ4
- Every structure of UniProt Q9VMN6
- Elsewhere: RCSB PDB 6EG1 · PDBe 6EG1 · UniProt Q59DZ4 · UniProt Q9VMN6
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