MolNFT v1 · #162561 · protein
PFRH5 bound to monoclonal antibodies R5.004 and R5.016
6RCU · Reticulocyte binding protein homologue 5: “PFRH5 bound to monoclonal antibodies R5.004 and R5.016”. X-ray diffraction, 17 pockets (best druggability 0.65). MolNFT v1 #162561 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6RCU
- Type
- protein
- Length
- 1,175 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticulocyte binding protein homologue 5; R5.004 heavy chain; R5.004 light chain; R5.016…
- UniProt
- Q8IFM5
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticulocyte binding protein homologue 5 | protein | 304 | 74% helix, 5% strand | Q8IFM5 |
| B | R5.004 heavy chain | protein | 222 | 9% helix, 53% strand | — |
| C | R5.004 light chain | protein | 211 | 7% helix, 49% strand | — |
| D | R5.016 light chain | protein | 210 | 5% helix, 48% strand | — |
| E | R5.016 heavy chain | protein | 228 | 9% helix, 48% strand | — |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.65 | 0.80 | 46 | empty |
| 2 | 100 | 0.65 | 0.90 | 29 | empty |
| 3 | 129 | 0.59 | 0.84 | 24 | empty |
| 4 | 177 | 0.51 | 0.78 | 22 | empty |
| 5 | 285 | 0.51 | 0.74 | 45 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2134 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1588 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 792 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 377 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6RCU · PfRH5 bound to monoclonal antibodies R5.004 and R5.016 · 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 6RCU · PDBe 6RCU · UniProt Q8IFM5
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