SMTL ID : 7t2b.2 (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: 4 residues within 4Å: Chain A: V.116, N.118, E.166, W.168 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.78 NAG.4: 2 residues within 4Å: Chain B: F.20, N.21 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: P.86, P.87, E.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.88, A:E.88 EDO.5: 3 residues within 4Å: Chain E: F.10, Y.212, T.229 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.229, E:T.229

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
F

B
G

C
H

D
I

E
J

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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