MolNFT v1 · #168711 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 251249
6WOZ: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 251249”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #168711 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6WOZ
- Type
- protein
- Length
- 2,948 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 251249 Fab heavy chain; 251249 Fab light chain
- UniProt
- A5K736
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | Reticulocyte binding protein 2B | protein | 297 | 77% helix, 3% strand | A5K736 |
| E | 251249 Fab heavy chain | protein | 229 | 9% helix, 56% strand | — |
| F, C, I, L | 251249 Fab light chain | protein | 213 | 6% helix, 49% strand | — |
| B, H | 251249 Fab heavy chain | protein | 227 | 6% helix, 55% strand | — |
| D, A | Reticulocyte binding protein 2B | protein | 296 | 76% helix, 3% strand | A5K736 |
| K | 251249 Fab heavy chain | protein | 226 | 7% helix, 54% strand | — |
| G | Reticulocyte binding protein 2B | protein | 298 | 75% helix, 2% strand | A5K736 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.80 | 0.82 | 108 | empty |
| 2 | 980 | 0.80 | 0.81 | 97 | empty |
| 3 | 1174 | 0.76 | 0.78 | 96 | empty |
| 4 | 1065 | 0.76 | 0.78 | 81 | empty |
| 5 | 570 | 0.65 | 0.76 | 50 | empty |
Interfaces
27 interfaces between chains.
- K–L · 1818 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1812 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1801 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 1774 Ų buried · 11 hydrogen bonds · protein-protein
- H–G · 891 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6WOZ · Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal… · the same entry in another collection · chain J against J, 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 6WOZ · PDBe 6WOZ · UniProt A5K736
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