SMTL ID : 7t2b.4 (3 other biounits)

Crystal structure of the 5F TCR in complex with HLA-DP4-Ply

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: H.16, V.116, N.118, E.166, H.167, W.168 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: R.76, N.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:N.78 NAG.4: 1 residues within 4Å: Chain B: N.21 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: H.16, R.17, V.116 Ligands: NAG-NAG.1, NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.17 EDO.5: 6 residues within 4Å: Chain B: E.70, R.77 Chain D: N.31, L.48, R.50 Chain E: G.97 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.50, B:E.70, B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciacchi, L. et al., CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity. Immunity (2023)

Release Date

2022-12-28

Peptides

HLA class II histocompatibility antigen, DP alpha 1 chain: A
HLA class II histocompatibility antigen, DP beta 1 chain: B
Pneumolysin-derived peptide: C
T cell receptor, 5F, alpha chain: D
T cell receptor, 5F, beta chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
Q

C
R

D
S

E
T

HLA class II histocompatibility antigen, DP alpha 1 chain

HLA class II histocompatibility antigen, DP beta 1 chain

Pneumolysin-derived peptide

T cell receptor, 5F, alpha chain

T cell receptor, 5F, beta chain

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