SMTL ID : 2zok.6 (5 other biounits)

Crystal structure of H-2Db in complex with JHMV epitope S510

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ABA- SER- LEU- TRP- ASN- GLY- PRO- HIS- LEU: 9-meric peptide from Spike glycoprotein(Non-covalent)

ABA-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU.1: 32 residues within 4Å: Chain C: M.5, Y.7, E.9, Y.45, Y.59, E.63, Q.65, K.66, G.69, 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, W.167, Y.171 Ligands: SO4.5 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:K.66, C:W.73, C:W.73, C:L.81, C:L.95, C:Y.123, C:T.143, C:W.147, C:A.152, C:Y.156, C:Y.159, C:W.167 Hydrogen bonds: C:Y.7, C:Y.7, C:Y.45, C:Y.59, C:E.63, C:Q.70, C:Q.70, C:S.77, C:N.80, C:Y.84, C:Q.97, C:Q.97, C:Y.156, C:Y.156, C:Y.171 Water bridges: C:S.24, C:K.66 Salt bridges: C:K.146 ABA-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU.2: 30 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.45, E.63, Q.65, K.66, G.69, 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, W.167, Y.171 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:K.66, A:W.73, A:W.73, A:L.81, A:L.95, A:Y.123, A:T.143, A:W.147, A:A.152, A:Y.156, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.45, A:E.63, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Y.84, A:Q.97, A:Q.97, A:K.146, A:Y.156, A:Y.156, A:Y.171, A:Y.171 Water bridges: A:S.24, A:K.66 Salt bridges: A:K.146

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

SO4.3: 4 residues within 4Å: Chain A: Q.87, H.93 Chain C: Q.87, H.93 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.87, C:Q.87 Water bridges: A:N.86, C:H.93 SO4.5: 3 residues within 4Å: Chain C: K.146 Ligands: ABA-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU.1, ABA-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU.1 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.146

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.6, F.8, Y.27, N.30 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.30 Water bridges: A:S.4, A:R.6, A:Y.27, A:Y.27, B:Y.64 GOL.6: 4 residues within 4Å: Chain C: R.6, F.8, Y.27, N.30 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:Y.64, C:S.4, C:Y.27, C:Y.27, C:N.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butler, N.S. et al., Structural and biological basis of CTL escape in coronavirus-infected mice. J Immunol. (2008)

Release Date

2008-06-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

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

Beta-2-microglobulin

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