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Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal antibody 6H1
Analyse Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BPE
- Type
- protein
- Length
- 2,194 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2, putative; Monoclonal antibody 6H1 Fab heavy chain…
- UniProt
- A5K736
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2, putative | protein | 299 | 79% helix, 3% strand | A5K736 |
| B | Monoclonal antibody 6H1 Fab heavy chain | protein | 209 | 5% helix, 48% strand | — |
| C | Monoclonal antibody 6H1 Fab light chain | protein | 199 | 6% helix, 44% strand | — |
| D | Reticulocyte binding protein 2, putative | protein | 302 | 76% helix, 3% strand | A5K736 |
| E | Monoclonal antibody 6H1 Fab heavy chain | protein | 208 | 5% helix, 42% strand | — |
| F | Monoclonal antibody 6H1 Fab light chain | protein | 198 | 6% helix, 50% strand | — |
| G | Reticulocyte binding protein 2, putative | protein | 302 | 76% helix, 3% strand | A5K736 |
| H | Monoclonal antibody 6H1 Fab heavy chain | protein | 113 | 0% helix, 42% strand | — |
| I | Monoclonal antibody 6H1 Fab light chain | protein | 67 | 0% helix, 15% strand | — |
| J | Reticulocyte binding protein 2, putative | protein | 297 | 71% helix, 3% strand | A5K736 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.80 | 0.92 | 42 | empty |
| 2 | 898 | 0.78 | 0.80 | 89 | empty |
| 3 | 440 | 0.78 | 0.86 | 52 | empty |
| 4 | 809 | 0.68 | 0.75 | 53 | empty |
| 5 | 609 | 0.67 | 0.77 | 42 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1842 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1731 Ų buried · 10 hydrogen bonds · protein-protein
- A–J · 1119 Ų buried · 3 hydrogen bonds · protein-protein
- H–I · 744 Ų buried · 4 hydrogen bonds · protein-protein
- G–J · 666 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6BPE · Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody… · 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 6BPE · PDBe 6BPE · UniProt A5K736
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