SMTL ID : 8trq.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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: 5 residues within 4Å: Chain A: V.116, V.117, N.118, E.166, W.168 No protein-ligand interaction detected (PLIP)

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: I.8, D.25, G.28, P.139, R.140, R.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.139 GOL.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: R.123, V.128, T.130, L.151, P.152, F.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:T.130, A:P.152 GOL.5: 5 residues within 4Å: Chain A: F.108, F.148 Chain B: L.147, I.148, Q.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.149, B:Q.149, B:Q.149 GOL.6: 4 residues within 4Å: Chain A: T.41, W.43, S.53, F.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.41, A:F.54 Water bridges: A:T.41 GOL.7: 4 residues within 4Å: Chain B: E.98, V.99, L.184, V.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.98, B:V.99 GOL.8: 7 residues within 4Å: Chain B: I.127, E.128, V.129, S.144, G.146, T.157, V.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.128, B:S.144 GOL.9: 6 residues within 4Å: Chain D: L.103, I.104, F.105 Chain E: L.44, R.45, L.46 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:L.46, D:L.103, D:F.105, D:F.105 GOL.10: 1 residues within 4Å: Chain E: G.164 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain E: P.123, P.124, E.125, Q.234, V.236 2 PLIP interactions: 2 interactions with chain E Water bridges: E:V.126, E:V.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
Vimentin: C
A07 TCR alpha chain: D
A07 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

A07 TCR alpha chain

A07 TCR beta chain

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