Research workbench
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 237235
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
- 6WM9
- Type
- protein
- Length
- 1,462 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 237235 Fab heavy chain; 237235 Fab light chain
- UniProt
- A5K736
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2B | protein | 296 | 75% helix, 3% strand | A5K736 |
| B | 237235 Fab heavy chain | protein | 225 | 5% helix, 50% strand | — |
| E | 237235 Fab heavy chain | protein | 222 | 8% helix, 51% strand | — |
| C, F | 237235 Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| D | Reticulocyte binding protein 2B | protein | 295 | 75% helix, 3% strand | A5K736 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.76 | 0.88 | 45 | empty |
| 2 | 1174 | 0.75 | 0.78 | 132 | empty |
| 3 | 718 | 0.67 | 0.75 | 73 | empty |
| 4 | 630 | 0.64 | 0.75 | 60 | empty |
| 5 | 139 | 0.51 | 0.80 | 27 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1993 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1852 Ų buried · 10 hydrogen bonds · protein-protein
- F–D · 655 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6WM9 · 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 6WM9 · PDBe 6WM9 · UniProt A5K736
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