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Heterotetramer structure of region II from plasmodium vivax duffy binding protein (pvdbp) bound to the ectodomain of the duffy antigen receptor for chemokines (darc)
Analyse Heterotetramer structure of region II from plasmodium vivax duffy binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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