Research workbench
Crystal structure of region II from plasmodium vivax duffy binding protein
Analyse Crystal structure of region II from plasmodium vivax duffy binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RRC
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duffy receptor
- UniProt
- P22290
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duffy receptor | protein | 276 | 66% helix, 1% strand | P22290 |
| B | Duffy receptor | protein | 279 | 67% helix, 1% strand | P22290 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.70 | 0.92 | 25 | EDO |
| 2 | 125 | 0.69 | 0.90 | 30 | EDO |
| 3 | 270 | 0.54 | 0.76 | 24 | PO4 |
| 4 | 149 | 0.43 | 0.75 | 21 | empty |
| 5 | 70 | 0.40 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 551 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3RRC · Crystal Structure of Region II from Plasmodium vivax Duffy Binding Protein · 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 B against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 3RRC · PDBe 3RRC · UniProt P22290
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