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

T cell recognition of citrullinated vimentin peptide presented by HLA-DR4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

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

Ligands

2 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: N.118, E.166, W.168 Chain B: D.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.2, B:D.2, B:D.2 NAG-NAG.2: 2 residues within 4Å: Chain A: N.78 Ligands: SO4.6 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.44, V.104, Y.150 Chain B: D.152 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.44, A:R.44, B:D.152, B:D.152 GOL.4: 6 residues within 4Å: Chain A: V.6, I.8, D.25, G.28, P.139, R.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.139, A:R.146 Water bridges: A:G.28 GOL.5: 3 residues within 4Å: Chain A: D.110, K.111, R.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.111, A:R.140, A:R.140 GOL.9: 4 residues within 4Å: Chain B: E.128, E.176, H.177, P.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.176, B:H.177 GOL.10: 2 residues within 4Å: Chain B: R.25, R.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.25, B:R.39, B:R.39 GOL.12: 6 residues within 4Å: Chain D: Y.42, R.63, K.80, Q.84, S.86, D.87 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.42, D:Y.42, D:Q.84 GOL.14: 7 residues within 4Å: Chain E: V.154, E.155, L.156, T.171, D.172, P.173, L.189 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.156, E:L.156

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 1 residues within 4Å: Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain A: R.123, N.124, K.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.124 Salt bridges: A:R.123, A:K.126 SO4.11: 3 residues within 4Å: Chain B: R.93, R.94, V.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Salt bridges: B:R.93 SO4.13: 5 residues within 4Å: Chain D: R.41, P.43, G.44, R.110 Chain E: R.109 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:R.109, D:G.44 Water bridges: D:R.41 Salt bridges: D:R.41, D:R.110 SO4.15: 6 residues within 4Å: Chain A: A.64, V.65 Chain E: D.30, Y.50, V.51, Q.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.30 SO4.16: 3 residues within 4Å: Chain E: V.165, H.166, S.167 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.166, E:S.167, E:S.167

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

NAG.8: 2 residues within 4Å: Chain B: N.19, E.22 No protein-ligand interaction detected (PLIP)

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
Vimentin: C
A03 TCR alpha chain: D
A03 TCR beta chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1 beta chain

Vimentin

A03 TCR alpha chain

A03 TCR beta chain

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