MolNFT v1 · #144298 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal antibody 4F7
6BPC · Reticulocyte binding protein 2, putative: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to monoclonal antibody 4F7”. X-ray diffraction, 16 pockets (best druggability 0.72). MolNFT v1 #144298 on GenesisL1: 3D…
- PDB
- 6BPC
- Type
- protein
- Length
- 1,430 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2, putative; Monoclonal antibody 4F7 Fab heavy chain…
- UniProt
- A5K736
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2, putative | protein | 296 | 76% helix, 3% strand | A5K736 |
| B | Monoclonal antibody 4F7 Fab heavy chain | protein | 213 | 6% helix, 54% strand | — |
| C | Monoclonal antibody 4F7 Fab light chain | protein | 212 | 4% helix, 50% strand | — |
| D | Reticulocyte binding protein 2, putative | protein | 286 | 79% helix, 3% strand | A5K736 |
| E | Monoclonal antibody 4F7 Fab heavy chain | protein | 212 | 6% helix, 53% strand | — |
| F | Monoclonal antibody 4F7 Fab light chain | protein | 211 | 5% helix, 51% strand | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.72 | 0.77 | 78 | empty |
| 2 | 601 | 0.62 | 0.74 | 59 | empty |
| 3 | 554 | 0.62 | 0.75 | 58 | empty |
| 4 | 226 | 0.53 | 0.77 | 35 | empty |
| 5 | 152 | 0.51 | 0.79 | 24 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1746 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1711 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 539 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 430 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6BPC · 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 6BPC · PDBe 6BPC · UniProt A5K736
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