Research workbench
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 243244
Analyse Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WNO
- Type
- protein
- Length
- 1,442 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 243244 Fab heavy chain; 243244 Fab light chain; Plasmodium vivax reticulocyte binding…
- UniProt
- A5K736
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 243244 Fab heavy chain | protein | 214 | 4% helix, 51% strand | — |
| C | 243244 Fab light chain | protein | 210 | 6% helix, 49% strand | — |
| A | Plasmodium vivax reticulocyte binding protein 2B | protein | 290 | 77% helix, 2% strand | A5K736 |
| D | Plasmodium vivax reticulocyte binding protein 2B | protein | 296 | 75% helix, 3% strand | A5K736 |
| E | 243244 Fab heavy chain | protein | 220 | 5% helix, 51% strand | — |
| F | 243244 Fab light chain | protein | 212 | 7% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.78 | 0.90 | 49 | empty |
| 2 | 303 | 0.77 | 0.88 | 56 | empty |
| 3 | 535 | 0.72 | 0.80 | 55 | empty |
| 4 | 58 | 0.71 | 0.97 | 19 | empty |
| 5 | 69 | 0.70 | 0.96 | 21 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2007 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1814 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 628 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 625 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 617 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 6WNO · Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal… · the same entry in another collection · chain B against B, 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 6WNO · PDBe 6WNO · UniProt A5K736
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