MolNFT v1 · #101552 · protein
Heterotrimer structure of region II from plasmodium vivax duffy binding protein (pvdbp) bound to the ectodomain of the duffy antigen receptor for chemokines (darc)
4NUU · Duffy receptor: “Heterotrimer structure of region II from plasmodium vivax duffy binding protein (pvdbp) bound to the…”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #101552 on GenesisL1: 3D structure, binding…
- PDB
- 4NUU
- Type
- protein
- Length
- 586 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duffy receptor; Duffy ANTIGEN/CHEMOKINE receptor
- UniProt
- P22290, Q16570
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duffy receptor | protein | 282 | 66% helix, 1% strand | P22290 |
| B | Duffy receptor | protein | 292 | 65% helix, 2% strand | P22290 |
| C | Duffy ANTIGEN/CHEMOKINE receptor | protein | 12 | 58% helix, 0% strand | Q16570 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.72 | 0.93 | 25 | empty |
| 2 | 132 | 0.70 | 0.91 | 30 | empty |
| 3 | 145 | 0.47 | 0.77 | 23 | empty |
| 4 | 109 | 0.37 | 0.74 | 18 | empty |
| 5 | 52 | 0.35 | 0.78 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 650 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 289 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4NUU · Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP)… · the same entry in another collection · chain A against A, TM-score 1.00
- P22290 · AlphaFold monomer V2.0 prediction for duffy receptor (P22290) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q16570 · AlphaFold monomer V2.0 prediction for atypical chemokine receptor 1 (Q16570) · a predicted model of the same protein · chain C against A, TM-score 0.67
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 P22290
- Every structure of UniProt Q16570
- Elsewhere: RCSB PDB 4NUU · PDBe 4NUU · UniProt P22290 · UniProt Q16570
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