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Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 273264
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
- 6WTU
- Type
- protein
- Length
- 2,898 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 273264 Fab heavy chain; 273264 Fab light chain
- UniProt
- A5K736
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 10 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2B | protein | 301 | 73% helix, 3% strand | A5K736 |
| K | 273264 Fab heavy chain | protein | 217 | 6% helix, 51% strand | — |
| L | 273264 Fab light chain | protein | 207 | 8% helix, 44% strand | — |
| B | 273264 Fab heavy chain | protein | 219 | 4% helix, 49% strand | — |
| E | 273264 Fab heavy chain | protein | 218 | 6% helix, 49% strand | — |
| I, C, F | 273264 Fab light chain | protein | 209 | 8% helix, 49% strand | — |
| H | 273264 Fab heavy chain | protein | 218 | 4% helix, 51% strand | — |
| G | Reticulocyte binding protein 2B | protein | 297 | 75% helix, 3% strand | A5K736 |
| J | Reticulocyte binding protein 2B | protein | 295 | 78% helix, 3% strand | A5K736 |
| D | Reticulocyte binding protein 2B | protein | 299 | 75% helix, 3% strand | A5K736 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.83 | 0.84 | 107 | empty |
| 2 | 526 | 0.80 | 0.87 | 63 | empty |
| 3 | 469 | 0.80 | 0.87 | 48 | empty |
| 4 | 642 | 0.71 | 0.79 | 76 | empty |
| 5 | 585 | 0.65 | 0.76 | 44 | empty |
Interfaces
25 interfaces between chains.
- B–C · 1670 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1619 Ų buried · 19 hydrogen bonds · protein-protein
- I–H · 1603 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1565 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1157 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6WTU · 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 6WTU · PDBe 6WTU · UniProt A5K736
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