SMTL ID : 9c6w.1 (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

7 x SO4: SULFATE ION

SO4.1: 4 residues within 4Å: Chain A: R.158, R.161, R.165 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.161 Salt bridges: A:R.158, A:R.161, A:R.165 SO4.2: 3 residues within 4Å: Chain A: H.76, R.165 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.60 Salt bridges: A:H.76, A:R.165 SO4.3: 2 residues within 4Å: Chain A: R.363, R.400 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.363 Salt bridges: A:R.400 SO4.4: 4 residues within 4Å: Chain A: H.336, I.338, T.344, R.346 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.336, A:R.346 SO4.5: 3 residues within 4Å: Chain A: S.82, K.83 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.82, A:K.83 Salt bridges: A:K.83 SO4.6: 3 residues within 4Å: Chain A: Q.231, S.232, G.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.232, A:S.232, A:G.235 SO4.7: 1 residues within 4Å: Chain A: R.28 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.28

8 x EDO: 1,2-ETHANEDIOL

EDO.8: 2 residues within 4Å: Chain A: V.3, M.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.4 EDO.9: 3 residues within 4Å: Chain A: N.42, T.98, E.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:E.99 EDO.10: 5 residues within 4Å: Chain A: V.34, Y.35, S.36, W.120, D.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.36, A:S.36, A:D.121 EDO.11: 5 residues within 4Å: Chain A: A.184, A.185, S.186, R.188, E.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.185, A:S.186, A:S.186, A:R.188 EDO.12: 3 residues within 4Å: Chain A: R.188, E.190, P.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.188, A:R.188 EDO.13: 2 residues within 4Å: Chain A: E.310, W.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.310 EDO.14: 5 residues within 4Å: Chain A: Y.88, Y.171, D.173, D.174 Ligands: EDO.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.88, A:D.174 Water bridges: A:S.148, A:Y.171, A:D.173 EDO.15: 4 residues within 4Å: Chain A: Y.88, A.355 Ligands: SO4.5, EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.88 Water bridges: A:Y.88

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.16: 6 residues within 4Å: Chain A: K.7, A.9, G.10, E.220, 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 PEG.17: 4 residues within 4Å: Chain A: D.59, N.108, H.109, V.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.110

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
A

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

Related Entries With Identical Sequence