SMTL ID : 6atf.2 (1 other biounit)

HLA-DRB1*1402 in complex with Vimentin59-71

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: V.116, N.118, E.166, H.167, W.168 Chain B: D.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.4, B:D.4

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

NAG.2: 3 residues within 4Å: Chain A: R.76, N.78 Chain B: L.55 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.76, A:N.78 Hydrophobic interactions: B:L.55

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain B: Q.72, R.73 Chain C: T.5, R.6, S.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.72, B:R.73, C:T.5, C:S.7 Water bridges: B:Q.72 EDO.4: 2 residues within 4Å: Chain B: F.134, Q.176 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: S.77, T.80 Chain B: H.34, N.35, E.37, L.55 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.80, B:N.35 Water bridges: B:E.37, B:E.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scally, S.W. et al., Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis. Ann. Rheum. Dis. (2017)

Release Date

2017-09-13

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
MHC class II antigen: B
Vimentin59-71: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

HLA class II histocompatibility antigen, DR alpha chain

MHC class II antigen

Vimentin59-71

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