Research workbench
Crystal structure of mouse CD3EPSILON in complex with antibody 2C11 Fab
Analyse Crystal structure of mouse CD3EPSILON in complex with antibody 2C11 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R08
- Type
- protein
- Length
- 511 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse anti-mouse CD3EPSILON antibody 2C11 light chain; Mouse anti-mouse CD3EPSILON…
- UniProt
- P22646
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Mouse anti-mouse CD3EPSILON antibody 2C11 light chain | protein | 213 | 6% helix, 40% strand | — |
| H | Mouse anti-mouse CD3EPSILON antibody 2C11 heavy chain | protein | 216 | 3% helix, 47% strand | — |
| E | T-cell surface glycoprotein CD3 epsilon chain | protein | 82 | 0% helix, 26% strand | P22646 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.55 | 0.83 | 19 | empty |
| 2 | 91 | 0.45 | 0.80 | 23 | empty |
| 3 | 131 | 0.41 | 0.75 | 23 | empty |
| 4 | 60 | 0.37 | 0.79 | 18 | empty |
| 5 | 73 | 0.35 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2054 Ų buried · 22 hydrogen bonds · protein-protein
- H–E · 772 Ų buried · 19 hydrogen bonds · protein-protein
- L–E · 202 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3R08 · Crystal structure of mouse cd3epsilon in complex with antibody 2C11 Fab · the same entry in another collection · chain L against L, TM-score 1.00
- P22646 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain E against A, TM-score 0.80
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 P22646
- Elsewhere: RCSB PDB 3R08 · PDBe 3R08 · UniProt P22646
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