SMTL ID : 8trr.2 (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

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

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

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

NAG.2: 3 residues within 4Å: Chain A: S.77, N.78 Chain B: L.53 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.78 Hydrophobic interactions: B:L.53

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: H.167, L.170, D.171, E.172, P.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.167 GOL.4: 4 residues within 4Å: Chain A: N.84, W.168 Chain B: D.2, T.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.84, A:N.84, A:W.168 Water bridges: A:N.84 GOL.6: 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

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

SO4.5: 2 residues within 4Å: Chain A: K.111, R.140 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.111, A:R.140 SO4.7: 2 residues within 4Å: Chain A: Y.150 Chain B: D.152 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.152, B:D.152, A:R.44 SO4.8: 1 residues within 4Å: Chain B: N.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.19 SO4.9: 5 residues within 4Å: Chain B: E.22, R.23, V.24, V.75, R.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.24, B:V.24 Salt bridges: B:R.80 SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.11: 2 residues within 4Å: Chain B: F.132, G.135 No protein-ligand interaction detected (PLIP) SO4.12: 5 residues within 4Å: Chain D: R.41, P.43, G.44, R.110 Chain E: R.109 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.44, E:R.109 Water bridges: D:R.41 Salt bridges: D:R.41, D:R.110 SO4.13: 6 residues within 4Å: Chain D: A.107, G.108, R.110 Chain E: Q.37, T.39, G.40 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Q.37, E:T.39, E:G.40, D:R.110 SO4.14: 4 residues within 4Å: Chain D: M.170 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 SO4.15: 2 residues within 4Å: Chain E: A.3, T.26 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
F

B
G

C
H

D
I

E
J

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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