SMTL ID : 8trl.2 (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- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN.1: 4 residues within 4Å: Chain A: R.76, S.77, N.78 Chain B: L.53 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, W.168 Chain B: D.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166, A:W.168 NAG.6: 2 residues within 4Å: Chain B: N.19, E.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.19

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

FMT.3: 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 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:Y.32, C:N.8, C:N.8

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: E.4 Chain B: F.18 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain A: V.6, I.8, D.25, G.28, P.139, R.140, E.141, R.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.139, A:R.146 Water bridges: A:R.140, A:E.141 GOL.7: 6 residues within 4Å: Chain B: H.81, G.84, V.85 Chain C: E.1 Chain D: S.27, G.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.84, D:G.28 GOL.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.9: 5 residues within 4Å: Chain A: F.108, F.148 Chain B: L.147, I.148, Q.149 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.149, B:Q.149 GOL.10: 6 residues within 4Å: Chain B: S.126, I.127, E.128, E.176, H.177, P.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.127 Water bridges: B:H.177 GOL.11: 3 residues within 4Å: Chain A: R.44, Y.150 Chain B: D.152 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.152, A:R.44, A:R.44 Water bridges: A:S.133 GOL.12: 2 residues within 4Å: Chain D: E.13, G.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.13 GOL.13: 7 residues within 4Å: Chain D: A.92, T.94, N.96, Q.97 Chain E: Y.34, R.96, Y.99 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Y.34, E:R.96, D:A.92, D:Q.97 Water bridges: E:R.96

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

ACT.14: 4 residues within 4Å: Chain E: L.31, N.52, N.53, R.70 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.52 Salt bridges: E:R.70

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
D

B
E

C
F

D
G

E
H

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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