MolNFT v1 · #144296 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal antibody 3E9
6BPA · Reticulocyte binding protein 2, putative: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal antibody 3E9”. X-ray diffraction, 1 ligand (BR), 12 pockets (best druggability 0.78). MolNFT v1 #144296 on…
- PDB
- 6BPA
- Type
- protein
- Length
- 1,448 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2, putative; Monoclonal antibody 3E9 Fab heavy chain…
- UniProt
- A5K736
- Ligands
- BR
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2, putative | protein | 297 | 75% helix, 3% strand | A5K736 |
| B | Monoclonal antibody 3E9 Fab heavy chain | protein | 217 | 7% helix, 55% strand | — |
| C | Monoclonal antibody 3E9 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| D | Reticulocyte binding protein 2, putative | protein | 296 | 75% helix, 3% strand | A5K736 |
| E | Monoclonal antibody 3E9 Fab heavy chain | protein | 215 | 4% helix, 56% strand | — |
| F | Monoclonal antibody 3E9 Fab light chain | protein | 211 | 6% helix, 50% strand | — |
Ligands and binding sites
- BR · Bromide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.78 | 0.80 | 71 | empty |
| 2 | 497 | 0.66 | 0.78 | 63 | empty |
| 3 | 368 | 0.64 | 0.79 | 52 | empty |
| 4 | 327 | 0.59 | 0.77 | 40 | empty |
| 5 | 359 | 0.55 | 0.74 | 48 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1802 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1746 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 626 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 602 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 377 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6BPA · 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 6BPA · PDBe 6BPA · UniProt A5K736
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