MolNFT v1 · #22199 · protein

Crystal structure of CD3GAMMAEPSILON heterodimer in complex with OKT3 Fab fragment

1SY6 · OKT3 Fab light chain: “Crystal structure of CD3GAMMAEPSILON heterodimer in complex with OKT3 Fab fragment”. X-ray diffraction, 8 pockets (best druggability 0.63). MolNFT v1 #22199 on GenesisL1: 3D structure, binding sites and…

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.

Pocket	Volume (Å³)	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 Å² buried · 18 hydrogen bonds · protein-protein
H–A · 504 Å² buried · 9 hydrogen bonds · protein-protein
L–A · 249 Å² 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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