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

HLA-DRB1*1402 in complex with Vimentin59-71

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain A: R.76, S.77, N.78 Chain B: L.55 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.55 Hydrogen bonds: A:R.76, A:N.78

4 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 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.72, B:R.73, C:S.7, C:S.7 EDO.4: 3 residues within 4Å: Chain B: E.178, H.179, P.180 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.179, B:H.179 EDO.5: 3 residues within 4Å: Chain B: F.134, T.174, T.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.174, B:T.174 EDO.6: 4 residues within 4Å: Chain B: R.135, Q.138, E.139, E.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.135

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 4 residues within 4Å: Chain B: R.25, V.26, S.44, D.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.25, B:R.25, B:V.26 PGE.8: 4 residues within 4Å: Chain B: I.129, E.130, S.146, T.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.129, B:E.130 Water bridges: B:I.129

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
A

B
B

C
C

HLA class II histocompatibility antigen, DR alpha chain

MHC class II antigen

Vimentin59-71

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