MolNFT v1 · #137981 · protein
Crystal structure of the erythrocyte-binding domain from plasmodium vivax reticulocyte-binding protein 2B (PVRBP2B)
5W53 · Reticulocyte binding protein 2, putative: “Crystal structure of the erythrocyte-binding domain from plasmodium vivax reticulocyte-binding protein 2B…”. X-ray diffraction, 2 ligands (K, SCN), 3 pockets (best druggability 0.79).…
- PDB
- 5W53
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2, putative
- UniProt
- A5K736
- Ligands
- K, SCN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Reticulocyte binding protein 2, putative | protein | 303 | 74% helix, 3% strand | A5K736 |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, B
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.79 | 0.80 | 80 | empty |
| 2 | 1129 | 0.78 | 0.80 | 90 | empty |
| 3 | 50 | 0.36 | 0.80 | 12 | SCN |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5W53 · 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 A5K736
- Elsewhere: RCSB PDB 5W53 · PDBe 5W53 · UniProt A5K736
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