Research workbench
PFRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments
Analyse PFRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PHU
- Type
- protein
- Length
- 1,172 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte-binding protein homolog 5; Monoclonal antibody R5.015 heavy chain…
- UniProt
- Q8IFM5
- Pockets
- 15 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte-binding protein homolog 5 | protein | 295 | 80% helix, 5% strand | Q8IFM5 |
| B | Monoclonal antibody R5.015 heavy chain | protein | 222 | 9% helix, 51% strand | — |
| C | Monoclonal antibody R5.015 light chain | protein | 212 | 8% helix, 49% strand | — |
| D | Monoclonal antibody R5.016 heavy chain | protein | 232 | 9% helix, 49% strand | — |
| E | Monoclonal antibody R5.016 light chain | protein | 211 | 6% helix, 50% strand | — |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.60 | 0.75 | 56 | empty |
| 2 | 167 | 0.55 | 0.80 | 23 | empty |
| 3 | 209 | 0.53 | 0.77 | 28 | empty |
| 4 | 246 | 0.53 | 0.76 | 27 | empty |
| 5 | 235 | 0.48 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2059 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1918 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 811 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 649 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 7PHU · PfRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IFM5 · AlphaFold monomer V2.0 prediction for reticulocyte-binding protein homolog 5 (Q8IFM5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8IFM5
- Elsewhere: RCSB PDB 7PHU · PDBe 7PHU · UniProt Q8IFM5
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