MolNFT v1 · #168671 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 243244
6WNO · 243244 Fab heavy chain: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 243244”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #168671 on GenesisL1: 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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