MolNFT v1 · #118496 · protein
Crystal structure of dbp in complex with inhibitory monoclonal antibody 2D10
5F3J · Duffy receptor: “Crystal structure of dbp in complex with inhibitory monoclonal antibody 2D10”. X-ray diffraction, 11 pockets (best druggability 0.69). MolNFT v1 #118496 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F3J
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duffy receptor; Antibody 2D10 single chain variable fragment
- UniProt
- P22290
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duffy receptor | protein | 251 | 60% helix, 1% strand | P22290 |
| B | Duffy receptor | protein | 249 | 63% helix, 2% strand | P22290 |
| C | Antibody 2D10 single chain variable fragment | protein | 228 | 3% helix, 43% strand | — |
| D | Antibody 2D10 single chain variable fragment | protein | 228 | 4% helix, 42% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.69 | 0.89 | 30 | empty |
| 2 | 188 | 0.69 | 0.87 | 35 | empty |
| 3 | 134 | 0.58 | 0.84 | 25 | empty |
| 4 | 176 | 0.45 | 0.74 | 26 | empty |
| 5 | 123 | 0.39 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 833 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 761 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 161 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 5F3J · Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10 · the same entry in another collection · chain A against A, TM-score 1.00
- P22290 · AlphaFold monomer V2.0 prediction for duffy receptor (P22290) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P22290
- Elsewhere: RCSB PDB 5F3J · PDBe 5F3J · UniProt P22290
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