SMTL ID : 9c6w.2 (1 other biounit)

Crystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (2 molecules/asymmetric unit)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

8 x SO4: SULFATE ION

SO4.1: 2 residues within 4Å: Chain A: S.82, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.82, A:K.83 Salt bridges: A:K.83 SO4.2: 3 residues within 4Å: Chain A: R.158, R.161, R.165 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.165 Water bridges: A:D.59, A:R.161 Salt bridges: A:R.158, A:R.161 SO4.3: 2 residues within 4Å: Chain A: H.76, R.165 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.76, A:R.165 SO4.4: 2 residues within 4Å: Chain A: R.70, R.106 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.106 SO4.5: 2 residues within 4Å: Chain A: F.95, T.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.96, A:T.96 SO4.6: 4 residues within 4Å: Chain A: H.336, I.338, T.344, R.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.344 Salt bridges: A:H.336, A:R.346 SO4.7: 2 residues within 4Å: Chain A: R.363, R.400 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.363, A:R.400 SO4.8: 3 residues within 4Å: Chain A: R.188, E.190, P.191 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.188

2 x CL: CHLORIDE ION

CL.9: 1 residues within 4Å: Chain A: S.232 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: S.339 Ligand excluded by PLIP

9 x EDO: 1,2-ETHANEDIOL

EDO.11: 4 residues within 4Å: Chain A: K.7, G.10, N.224, K.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.7, A:K.7, A:G.10, A:N.224 EDO.12: 2 residues within 4Å: Chain A: V.3, M.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.4 EDO.13: 3 residues within 4Å: Chain A: N.42, T.98, E.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.99 EDO.14: 1 residues within 4Å: Chain A: R.28 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain A: E.376, T.377, K.387 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.377, A:T.377, A:T.377, A:K.387 Water bridges: A:V.375 EDO.16: 6 residues within 4Å: Chain A: Y.88, F.152, Y.171, D.173, D.174 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.88, A:D.173 Water bridges: A:Y.88, A:Y.88 EDO.17: 3 residues within 4Å: Chain A: D.174, A.355 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.18: 2 residues within 4Å: Chain A: K.265, D.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.266, A:D.266 EDO.19: 5 residues within 4Å: Chain A: A.184, A.185, S.186, R.188, E.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.185, A:S.186, A:R.188, A:R.188, A:E.190

1 x P3G: 3,6,9,12,15-PENTAOXAHEPTADECANE

P3G.20: 3 residues within 4Å: Chain A: T.331, P.413, T.415 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL

GOL.21: 3 residues within 4Å: Chain A: G.23, C.228, Y.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, R. et al., Structural and biochemical analysis of highly similar HLA-B allotypes differentially associated with type 1 diabetes. J.Biol.Chem. (2024)

Release Date

2024-09-04

Peptides

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

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