MolNFT v1 · #101553 · protein
Heterotetramer structure of region II from plasmodium vivax duffy binding protein (pvdbp) bound to the ectodomain of the duffy antigen receptor for chemokines (darc)
4NUV · Duffy receptor: “Heterotetramer structure of region II from plasmodium vivax duffy binding protein (pvdbp) bound to the…”. X-ray diffraction, 9 pockets (best druggability 0.71). MolNFT v1 #101553 on GenesisL1: 3D structure, binding…
- PDB
- 4NUV
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duffy receptor; Duffy ANTIGEN/CHEMOKINE receptor
- UniProt
- P22290, Q16570
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duffy receptor | protein | 288 | 64% helix, 1% strand | P22290 |
| B | Duffy receptor | protein | 288 | 66% helix, 1% strand | P22290 |
| C, D | Duffy ANTIGEN/CHEMOKINE receptor | protein | 12 | 58% helix, 0% strand | Q16570 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.71 | 0.91 | 28 | empty |
| 2 | 106 | 0.70 | 0.93 | 25 | empty |
| 3 | 158 | 0.45 | 0.75 | 27 | empty |
| 4 | 92 | 0.42 | 0.78 | 21 | empty |
| 5 | 65 | 0.41 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–D · 666 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 658 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 125 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4NUV · Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP)… · the same entry in another collection · chain D against D, TM-score 1.00
- P22290 · AlphaFold monomer V2.0 prediction for duffy receptor (P22290) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q16570 · AlphaFold monomer V2.0 prediction for atypical chemokine receptor 1 (Q16570) · a predicted model of the same protein · chain D against A, TM-score 0.71
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 4NUV · PDBe 4NUV · UniProt P22290 · UniProt Q16570
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