MolNFT v1 · #168649 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 241242
6WN1: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 241242”. X-ray diffraction, 14 pockets (best druggability 0.65). MolNFT v1 #168649 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6WN1
- Type
- protein
- Length
- 1,192 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 241242 Fab heavy chain; 241242 Fab light chain
- UniProt
- A5K736
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2B | protein | 295 | 76% helix, 3% strand | A5K736 |
| B | 241242 Fab heavy chain | protein | 221 | 4% helix, 51% strand | — |
| C | 241242 Fab light chain | protein | 211 | 8% helix, 49% strand | — |
| F | 241242 Fab light chain | protein | 111 | 0% helix, 46% strand | — |
| D | Reticulocyte binding protein 2B | protein | 235 | 77% helix, 2% strand | A5K736 |
| E | 241242 Fab heavy chain | protein | 119 | 0% helix, 43% strand | — |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.65 | 0.91 | 28 | empty |
| 2 | 361 | 0.62 | 0.78 | 53 | empty |
| 3 | 198 | 0.60 | 0.82 | 35 | empty |
| 4 | 391 | 0.59 | 0.75 | 32 | empty |
| 5 | 356 | 0.57 | 0.75 | 32 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1744 Ų buried · 11 hydrogen bonds · protein-protein
- F–E · 793 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 733 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 682 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 657 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6WN1 · Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal… · 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 6WN1 · PDBe 6WN1 · UniProt A5K736
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