SMTL ID : 5jwd.1

Crystal structure of H-2Db in complex with the LCMV-derived GP392-401 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TRP- LEU- VAL- THR- ASN- GLY- SER- TYR- LEU: Pre-glycoprotein polyprotein GP complex(Non-covalent)

TRP-LEU-VAL-THR-ASN-GLY-SER-TYR-LEU.1: 31 residues within 4Å: Chain A: Y.7, E.9, Y.22, S.24, Y.59, R.62, E.63, K.66, Q.70, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, F.116, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:Y.59, A:W.73, A:W.73, A:W.73, A:V.76, A:V.76, A:L.81, A:L.95, A:Y.123, A:T.143, A:W.147, A:Y.159, A:Y.159, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Q.97, A:Q.97, A:K.146, A:S.150, A:S.150, A:Y.156, A:Y.159, A:Y.171, A:Y.171 Water bridges: A:Y.156, A:Y.156 Salt bridges: A:K.146 pi-Cation interactions: A:K.66

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.8, Y.27, N.30 Chain B: F.56, K.58, Y.63 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.63, B:Y.63, A:N.30 GOL.3: 2 residues within 4Å: Chain A: Y.85, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.87 GOL.4: 7 residues within 4Å: Chain A: P.235, A.236, G.237, D.238, G.239, T.240, F.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.236, A:G.237, A:G.239, A:T.240, A:T.240

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain B: R.12, H.13 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.12, B:H.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hafstrand, I. et al., Crystal structures of H-2Db in complex with the LCMV-derived peptides GP92 and GP392 explain pleiotropic effects of glycosylation on antigen presentation and immunogenicity. PLoS ONE (2017)

Release Date

2017-05-24

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

H-2 class I histocompatibility antigen, D-B alpha chain

Beta-2-microglobulin

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