Research workbench
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 241242
Analyse Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.