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Crystal structure of the erythrocyte-binding domain from plasmodium vivax reticulocyte-binding protein 2A (PVRBP2A)
Analyse Crystal structure of the erythrocyte-binding domain from plasmodium vivax… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z8N
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte-binding protein 2A
- UniProt
- A5JZ09
- Ligands
- MG, CA, CL
- Pockets
- 8 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte-binding protein 2A | protein | 298 | 80% helix, 3% strand | A5JZ09 |
| B | Reticulocyte-binding protein 2A | protein | 284 | 81% helix, 4% strand | A5JZ09 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.49 | 0.82 | 16 | CL |
| 2 | 109 | 0.45 | 0.78 | 18 | empty |
| 3 | 86 | 0.45 | 0.80 | 18 | empty |
| 4 | 106 | 0.41 | 0.76 | 20 | empty |
| 5 | 109 | 0.40 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1408 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4Z8N · Crystal structure of the erythrocyte-binding domain from Plasmodium vivax… · 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 A5JZ09
- Elsewhere: RCSB PDB 4Z8N · PDBe 4Z8N · UniProt A5JZ09
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