MolNFT v1 · #168772 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 283284
6WQO: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 283284”. X-ray diffraction, 19 pockets (best druggability 0.81). MolNFT v1 #168772 on GenesisL1: 3D structure, binding sites and pockets…
- 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
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