SMTL ID : 2zol.3 (2 other biounits)

Crystal structure of H-2Db in complex with the W513S variant of JHMV epitope S510

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1: 31 residues within 4Å: Chain A: M.5, Y.7, Y.45, E.63, K.66, Q.70, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, L.114, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, W.167, Y.171 Ligands: SO4.2, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.73, A:W.73, A:L.81, A:L.95, A:L.114, A:Y.123, A:T.143, A:W.147, A:A.152, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.45, A:E.63, A:K.66, 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 Salt bridges: A:K.146 ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3: 31 residues within 4Å: Chain C: M.5, Y.7, Y.45, E.63, K.66, Q.70, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171 Ligands: ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1, SO4.2 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: 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.159, C:W.167 Hydrogen bonds: C:Y.7, C:Y.7, C:Y.45, C:Y.45, C:E.63, C:K.66, C:Q.70, C:Q.70, C:S.77, C:N.80, C:Q.97, C:Q.97, C:K.146, C:Y.156, C:Y.159, C:Y.171 Salt bridges: C:K.146

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

SO4.2: 6 residues within 4Å: Chain A: K.146 Chain C: K.146 Ligands: ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.1, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3, ABA-SER-LEU-SER-ASN-GLY-PRO-HIS-LEU.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.146, C:K.146

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
C

C
A

B
D

D
B

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

Beta-2-microglobulin

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