SMTL ID : 8tw6.1

TCR in nanodisc ND-II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-2-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain G: N.52, F.64 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL

CLR.2: 10 residues within 4Å: Chain A: F.40, V.44, T.47, A.48 Chain B: L.257, V.260 Chain C: L.284 Chain G: V.124, V.128 Ligands: CLR.3 10 PLIP interactions: 5 interactions with chain A, 2 interactions with chain G, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.40, A:F.40, A:V.44, A:V.44, A:T.47, G:V.124, G:V.128, B:L.257, B:V.260, C:L.284 CLR.3: 9 residues within 4Å: Chain A: Y.33, F.40 Chain C: V.274, S.276, A.277, Y.281 Chain G: A.113, F.120 Ligands: CLR.2 7 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: C:V.274, C:A.277, G:A.113, G:F.120, A:F.40, A:F.40 Hydrogen bonds: C:S.276

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.4: 2 residues within 4Å: Chain G: N.92, S.94 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Notti, R.Q. et al., The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex. Biorxiv (2024)

Release Date

2024-10-02

Peptides

T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP: AH
TCR alpha: B
T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY: C
T-cell surface glycoprotein CD3 epsilon chain: DE
T-cell surface glycoprotein CD3 delta chain: F
T-cell surface glycoprotein CD3 gamma chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

H
X

B
A

C
B

D
E

E
F

F
D

G
G

Membrane

We predict this structure to be a membrane protein.
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T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP

TCR alpha

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY

T-cell surface glycoprotein CD3 epsilon chain

T-cell surface glycoprotein CD3 delta chain

T-cell surface glycoprotein CD3 gamma chain

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