SMTL ID : 6v13.1

immune receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

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

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.78 No protein-ligand interaction detected (PLIP) NAG.2: 5 residues within 4Å: Chain A: V.116, N.118, E.166, H.167, W.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.116 Hydrogen bonds: A:N.118, A:W.168 NAG.5: 3 residues within 4Å: Chain A: E.3 Chain B: N.19, E.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.19

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.44, Y.150 Chain B: D.152 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.152, A:R.44, A:R.44 GOL.4: 6 residues within 4Å: Chain A: I.8, D.25, D.27, G.28, P.139, R.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.139, A:R.146 GOL.6: 2 residues within 4Å: Chain B: R.72, D.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.76, B:D.76 GOL.7: 4 residues within 4Å: Chain B: D.76, H.81 Chain C: R.4 Chain D: Y.30 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.4, C:R.4, B:H.81 Water bridges: B:D.76 GOL.8: 5 residues within 4Å: Chain D: E.63, A.64, T.65, H.74, Q.76 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.63, D:T.65, D:S.72, D:S.72, D:Q.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, J.J. et al., The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR. Sci Immunol (2021)

Release Date

2020-11-25

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1-4 beta chain: B
Fibrinogen beta 74cit69-81: C
G08 TCR alpha chain: D
G08 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, DRB1-4 beta chain

Fibrinogen beta 74cit69-81

G08 TCR alpha chain

G08 TCR beta chain

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