SMTL ID : 5nig.1

Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: H.33, V.42, R.44, S.133, E.134, Y.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.33, A:S.133 Water bridges: A:R.44, A:S.133 MPD.4: 7 residues within 4Å: Chain B: Q.70, K.71, A.74, T.77 Chain C: K.5, A.6, V.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.5, C:V.7 Water bridges: C:K.5 Hydrophobic interactions: B:A.74 MPD.5: 2 residues within 4Å: Chain C: N.13, L.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.15 Hydrogen bonds: C:N.13

1 x URE: UREA(Non-functional Binders)

URE.2: 4 residues within 4Å: Chain B: R.23, V.24, V.75, R.80 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.24, B:V.24, B:R.80, B:R.80 Water bridges: B:R.23, B:D.76, B:D.76

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

PGE.3: 8 residues within 4Å: Chain A: N.94 Chain B: N.120, G.121, N.150, D.152, T.154, F.155, Q.156 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.120, B:G.121, B:N.150, A:N.94, A:N.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pieper, J. et al., Memory T cells specific to citrullinated alpha-enolase are enriched in the rheumatic joint. J. Autoimmun. (2018)

Release Date

2018-06-13

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1-4 beta chain: B
Alpha-enolase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1-4 beta chain

Alpha-enolase

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