Research workbench
PFRH5-binding monoclonal antibody R5.004
Analyse PFRH5-binding monoclonal antibody R5.004 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RCO
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R5.004 heavy chain; R5.004 light chain
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | R5.004 heavy chain | protein | 221 | 7% helix, 54% strand | — |
| B | R5.004 light chain | protein | 214 | 7% helix, 51% strand | — |
| C | R5.004 heavy chain | protein | 222 | 8% helix, 54% strand | — |
| D | R5.004 light chain | protein | 215 | 7% helix, 51% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.73 | 0.76 | 100 | GOL |
| 2 | 178 | 0.55 | 0.80 | 24 | empty |
| 3 | 158 | 0.48 | 0.77 | 34 | GOL |
| 4 | 156 | 0.42 | 0.74 | 32 | GOL |
| 5 | 88 | 0.42 | 0.78 | 18 | ACT, GOL |
Interfaces
5 interfaces between chains.
- C–D · 1898 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1852 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6RCO · PfRH5-binding monoclonal antibody R5.004 · 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
- Elsewhere: RCSB PDB 6RCO · PDBe 6RCO
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