SMTL ID : 7nze.1

Crystal structure of HLA-DR4 in complex with a human collagen type II peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: V.115, V.116, N.117, E.165, H.166, W.167 Chain B: D.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.2, A:N.117, A:W.167 Hydrophobic interactions: A:E.165 Water bridges: A:W.167 NAG.3: 4 residues within 4Å: Chain B: N.19, G.20, T.21, E.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.19 NAG.5: 7 residues within 4Å: Chain C: V.115, V.116, N.117, E.165, H.166, W.167 Chain D: D.2 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.167 Hydrogen bonds: C:N.117, C:E.165, C:W.167

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: V.5, I.7, D.24, D.26, G.27, P.138, R.139, E.140, R.145 Chain B: K.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.27, A:R.139 Water bridges: A:D.26, A:E.140, B:K.12 GOL.4: 5 residues within 4Å: Chain A: R.43, V.103, S.132, Y.149 Chain B: D.152 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:T.154 Hydrogen bonds: A:R.43, A:R.43 GOL.6: 4 residues within 4Å: Chain D: R.94, V.95, Y.96, S.179 No protein-ligand interaction detected (PLIP) GOL.7: 9 residues within 4Å: Chain A: E.171 Chain D: I.127, E.128, V.129, S.144, G.146, L.147, T.157, V.159 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.127, D:V.129, D:S.144, D:T.157, D:T.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ge, C. et al., Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor. Ann Rheum Dis (2022)

Release Date

2022-06-08

Peptides

HLA class II histocompatibility antigen, DR alpha chain: AC
HLA class II histocompatibility antigen DR beta chain: BD
Collagen alpha-1(II) chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

B
BBB

D
DDD

E
EEE

F
FFF

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen DR beta chain

Collagen alpha-1(II) chain

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