SMTL ID : 6v18.1

immune receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

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

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: V.116, N.118, E.166, W.168 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.116 Hydrogen bonds: A:N.118, A:E.166, A:W.168, B:D.2 Water bridges: B:D.2 NAG.4: 3 residues within 4Å: Chain A: E.3 Chain B: N.19, E.22 No protein-ligand interaction detected (PLIP)

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:D.25, A:G.28, A:R.140, A:R.146 GOL.3: 4 residues within 4Å: Chain A: R.44, V.104, 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.5: 4 residues within 4Å: Chain A: F.108 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.6: 5 residues within 4Å: Chain B: E.69, Q.70 Chain D: K.51, I.53 Chain E: N.99 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: E:N.99, D:K.51, B:E.69, B:E.69 GOL.7: 7 residues within 4Å: Chain D: K.135, S.136, W.180, S.181, N.182 Chain E: F.126, L.144 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.135, D:S.136, D:S.136 GOL.8: 5 residues within 4Å: Chain D: E.65, A.66, T.67, H.76, Q.78 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.65, D:E.65, D:T.67, D:H.76, D:H.76 GOL.9: 1 residues within 4Å: Chain D: K.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.17 Water bridges: D:K.17 GOL.10: 3 residues within 4Å: Chain D: E.44, G.45, Q.47 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.45 Water bridges: E:F.103, E:F.103 GOL.11: 3 residues within 4Å: Chain D: Q.10, T.12, K.162 No protein-ligand interaction detected (PLIP) GOL.12: 5 residues within 4Å: Chain A: Q.57 Chain D: K.102 Chain E: I.53, V.54, N.55 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.57, E:N.55 GOL.13: 5 residues within 4Å: Chain E: N.7, Y.8, A.105, G.106, R.108 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.8 GOL.14: 5 residues within 4Å: Chain E: V.153, D.171, P.172, P.174, L.188 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.172 Water bridges: E:V.153 GOL.15: 4 residues within 4Å: Chain E: V.159, V.194, S.195, F.198 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.195

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: C
M141 TCR alpha chain: D
M141 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

M141 TCR alpha chain

M141 TCR beta chain

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