SMTL ID : 8trl.1 (1 other biounit)

T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 1 residues within 4Å: Chain A: N.78 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.118, E.166, H.167, W.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118, A:W.168 NAG.8: 2 residues within 4Å: Chain B: N.19, E.22 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.123, F.153, L.154, Y.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.154 Salt bridges: A:R.123 ACT.6: 4 residues within 4Å: Chain A: Q.57, L.60 Chain E: S.56, K.58 1 PLIP interactions: 1 interactions with chain E Water bridges: E:K.58

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 8 residues within 4Å: Chain A: A.61, N.62, V.65 Chain C: G.7, N.8 Chain D: N.93 Chain E: Y.32, Y.99 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: D:N.93, E:Y.32, E:Y.32, C:N.8 FMT.5: 4 residues within 4Å: Chain A: F.51, A.52, S.53 Chain C: E.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.1 FMT.10: 6 residues within 4Å: Chain E: D.63, D.64, Q.65, F.66, S.67, R.81 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: I.8, D.25, G.28, P.139, R.140, E.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25, A:G.28 Water bridges: A:D.27, A:D.27 GOL.9: 6 residues within 4Å: Chain B: S.126, I.127, E.128, E.176, H.177, P.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loh, T.J. et al., The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4. Nat Commun (2024)

Release Date

2024-07-31

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1 beta chain: B
Alpha-enolase: C
RA2.7 TCR alpha chain: D
RA2.7 TCR beta chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

E
J

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1 beta chain

Alpha-enolase

RA2.7 TCR alpha chain

RA2.7 TCR beta chain

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