MolNFT v1 · #168624 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 237235
6WM9: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 237235”. X-ray diffraction, 14 pockets (best druggability 0.76). MolNFT v1 #168624 on GenesisL1: 3D structure, binding sites and pockets…
- 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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