MolNFT v1 · #168874 · protein
Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 258259
6WTV: “Plasmodium vivax reticulocyte binding protein 2B (PVRBP2B) bound to human monoclonal antibody 258259”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #168874 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6WTV
- Type
- protein
- Length
- 2,804 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein 2B; 258259 Fab light chain; 258259 Fab heavy chain
- UniProt
- A5K736
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 12 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein 2B | protein | 299 | 74% helix, 3% strand | A5K736 |
| C | 258259 Fab light chain | protein | 209 | 8% helix, 49% strand | — |
| B | 258259 Fab heavy chain | protein | 215 | 1% helix, 49% strand | — |
| G | Reticulocyte binding protein 2B | protein | 295 | 75% helix, 3% strand | A5K736 |
| H | 258259 Fab heavy chain | protein | 201 | 1% helix, 49% strand | — |
| I | 258259 Fab light chain | protein | 188 | 4% helix, 49% strand | — |
| J | Reticulocyte binding protein 2B | protein | 296 | 75% helix, 3% strand | A5K736 |
| K | 258259 Fab heavy chain | protein | 197 | 2% helix, 51% strand | — |
| L | 258259 Fab light chain | protein | 181 | 5% helix, 49% strand | — |
| E | 258259 Fab heavy chain | protein | 214 | 5% helix, 50% strand | — |
| F | 258259 Fab light chain | protein | 206 | 8% helix, 49% strand | — |
| D | Reticulocyte binding protein 2B | protein | 303 | 71% helix, 3% strand | A5K736 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.85 | 0.86 | 102 | empty |
| 2 | 942 | 0.81 | 0.83 | 81 | empty |
| 3 | 637 | 0.71 | 0.79 | 73 | empty |
| 4 | 384 | 0.64 | 0.78 | 52 | empty |
| 5 | 219 | 0.63 | 0.83 | 34 | empty |
Interfaces
24 interfaces between chains.
- E–F · 1650 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 1610 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1521 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1487 Ų buried · 10 hydrogen bonds · protein-protein
- G–D · 954 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6WTV · 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 6WTV · PDBe 6WTV · UniProt A5K736
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