SMTL ID : 9bbc.1

TCR GDN detergent micelle

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: I.26, N.41 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain F: K.51, N.52, T.54, F.64 No protein-ligand interaction detected (PLIP)

3 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.2: 1 residues within 4Å: Chain B: N.84 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain C: F.22, K.23, P.25, N.38, T.76, I.78, Y.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.79 NAG-NAG-BMA.5: 5 residues within 4Å: Chain C: S.40, N.74, K.80, D.81, E.83 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: T.77, N.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.77 NAG.7: 1 residues within 4Å: Chain A: N.166 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: D.152, N.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.200 NAG.9: 2 residues within 4Å: Chain A: N.208, N.211 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.208 NAG.11: 3 residues within 4Å: Chain F: S.90, Q.91, N.92 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL

CLR.10: 11 residues within 4Å: Chain A: L.257, A.261, N.264, L.265 Chain F: V.128, F.135 Chain H: F.40, V.44, T.47, A.48 Ligands: CLR.12 7 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: F:V.128, F:F.135, F:F.135, A:A.261, A:L.265, A:L.265, H:V.44 CLR.12: 9 residues within 4Å: Chain B: S.276, A.277 Chain F: T.114, G.117, A.121 Chain H: Y.33, G.37, F.40 Ligands: CLR.10 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: B:A.277, H:Y.33, H:Y.33, H:Y.33, H:Y.33, H:F.40, F:A.121

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

TCRa: A
TCRb: B
T-cell surface glycoprotein CD3 delta chain: C
T-cell surface glycoprotein CD3 epsilon chain: DE
T-cell surface glycoprotein CD3 gamma chain: F
T-cell surface glycoprotein CD3 zeta chain: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

G
X

H
Y

Membrane

We predict this structure to be a membrane protein.
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TCRa

TCRb

T-cell surface glycoprotein CD3 delta chain

T-cell surface glycoprotein CD3 epsilon chain

T-cell surface glycoprotein CD3 gamma chain

T-cell surface glycoprotein CD3 zeta chain

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