Research workbench
Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant epidermal growth factor receptor, egfrviii, at room temperature
Analyse Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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