Research workbench
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 283284
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
- 6WQO
- Type
- protein
- Length
- 1,431 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 283284 Fab heavy chain; 283284 Fab light chain
- UniProt
- A5K736
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2B | protein | 291 | 77% helix, 3% strand | A5K736 |
| D | Reticulocyte binding protein 2B | protein | 293 | 75% helix, 3% strand | A5K736 |
| E | 283284 Fab heavy chain | protein | 212 | 3% helix, 50% strand | — |
| F | 283284 Fab light chain | protein | 210 | 6% helix, 49% strand | — |
| B | 283284 Fab heavy chain | protein | 212 | 8% helix, 50% strand | — |
| C | 283284 Fab light chain | protein | 213 | 6% helix, 49% strand | — |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.81 | 0.89 | 65 | empty |
| 2 | 115 | 0.66 | 0.89 | 21 | empty |
| 3 | 118 | 0.63 | 0.87 | 22 | empty |
| 4 | 166 | 0.61 | 0.84 | 29 | empty |
| 5 | 455 | 0.58 | 0.74 | 55 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1711 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1676 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1197 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 640 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 639 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6WQO · 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 6WQO · PDBe 6WQO · UniProt A5K736
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.