MolNFT v1 · #9830 · protein
Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant epidermal growth factor receptor, egfrviii, at room temperature
1I8I · Epidermal growth factor receptor antibody MR1SCFV light…: “Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant epidermal growth factor…”. X-ray diffraction, 2 pockets (best druggability 0.28). MolNFT v1…
- PDB
- 1I8I
- Type
- protein
- Length
- 234 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor antibody MR1SCFV light chain; Epidermal growth factor…
- UniProt
- Q8R028, P18529
- Pockets
- 2 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor antibody MR1SCFV light chain | protein | 106 | 3% helix, 48% strand | Q8R028 |
| B | Epidermal growth factor receptor antibody MR1SCFV heavy chain | protein | 119 | 5% helix, 55% strand | P18529 |
| C | Epidermal growth factor receptor, egfrviii peptide antigen | protein | 9 | 0% helix, 11% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.28 | 0.73 | 17 | empty |
| 2 | 58 | 0.25 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 875 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 450 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 199 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1I8I · Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant epidermal… · the same entry in another collection · chain A against A, TM-score 1.00
- P18529 · AlphaFold monomer V2.0 prediction for ig heavy chain V region 5-76 (P18529) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q8R028
- Every structure of UniProt P18529
- Elsewhere: RCSB PDB 1I8I · PDBe 1I8I · UniProt Q8R028 · UniProt P18529
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