SMTL ID : 4l8b.1

Crystal structure of the H2Db in complex with the NP-N5H peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- SER- ASN- GLU- HIS- MET- GLU- THR- MET: NP-N5H peptide(Non-covalent)

ALA-SER-ASN-GLU-HIS-MET-GLU-THR-MET.1: 26 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.45, E.63, K.66, Q.70, W.73, F.74, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, F.116, Y.123, T.143, K.146, W.147, S.150, Y.156, Y.159, W.167, Y.171 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:K.66, A:W.73, A:V.76, A:L.81, A:K.146, A:Y.159, A:W.167 Hydrogen bonds: 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:T.143, A:K.146, A:Y.156, A:Y.156, A:Y.159, A:Y.171 Water bridges: A:S.24, A:E.63, A:Q.97, A:S.150, A:Y.156, A:Y.159 Salt bridges: A:K.146, A:K.146

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

SO4.2: 1 residues within 4Å: Chain A: R.194 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.194 SO4.3: 3 residues within 4Å: Chain A: P.20, R.75 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.75

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 9 residues within 4Å: Chain A: S.13, P.20, R.75, L.78, R.79, L.82, G.91, H.93 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.13, A:H.93 Water bridges: A:Y.118

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain B: S.57, K.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.58 Water bridges: B:S.57, B:S.57, B:D.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valkenburg, S.A. et al., Acute emergence and reversion of influenza A virus quasispecies within CD8(+) T cell antigenic peptides. Nat Commun (2013)

Release Date

2013-10-16

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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