Research workbench
Crystal structure of CD3GAMMAEPSILON heterodimer in complex with OKT3 Fab fragment
Analyse Crystal structure of CD3GAMMAEPSILON heterodimer in complex with OKT3 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SY6
- Type
- protein
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OKT3 Fab light chain; OKT3 Fab heavy chain; T-cell surface glycoprotein CD3 GAMMA/EPSILON…
- UniProt
- P09693, P07766
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | OKT3 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| H | OKT3 Fab heavy chain | protein | 219 | 10% helix, 52% strand | — |
| A | T-cell surface glycoprotein CD3 GAMMA/EPSILON chain | protein | 168 | 6% helix, 47% strand | P09693, P07766 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.63 | 0.78 | 47 | empty |
| 2 | 495 | 0.60 | 0.74 | 59 | empty |
| 3 | 154 | 0.52 | 0.80 | 28 | empty |
| 4 | 151 | 0.42 | 0.74 | 23 | empty |
| 5 | 74 | 0.35 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1945 Ų buried · 18 hydrogen bonds · protein-protein
- H–A · 504 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 249 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1SY6 · Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment · the same entry in another collection · chain L against L, TM-score 1.00
- P07766 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain A against A, TM-score 0.49
- P09693 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 gamma chain (P09693) · a predicted model of the same protein · chain A against A, TM-score 0.46
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 P09693
- Every structure of UniProt P07766
- Elsewhere: RCSB PDB 1SY6 · PDBe 1SY6 · UniProt P09693 · UniProt P07766
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