SMTL ID : 4l8d.2 (1 other biounit)

Crystal structure of the H2Db in complex with the NP-N5D peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- SER- ASN- GLU- ASP- MET- GLU- THR- MET: NP-N5D peptide(Non-covalent)

ALA-SER-ASN-GLU-ASP-MET-GLU-THR-MET.1: 24 residues within 4Å: Chain A: M.5, Y.7, Y.45, E.63, K.66, Q.70, W.73, S.77, N.80, L.81, Y.84, L.95, F.116, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, W.167, Y.171 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.81, A:A.152, A:Y.156, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.45, A:Y.45, A:E.63, A:K.66, A:Q.70, A:S.77, A:N.80, A:K.146, A:K.146, A:S.150, A:Y.171, A:Y.171 Water bridges: A:S.24, A:Q.70, A:W.73, A:Y.159 Salt bridges: A:K.146

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

SO4.2: 4 residues within 4Å: Chain A: R.111, Y.113, Q.115 Chain B: K.58 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.113, A:Q.115 Water bridges: A:R.111 Salt bridges: A:R.111, B:K.58 SO4.3: 3 residues within 4Å: Chain A: Q.141, R.145, E.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.141, A:E.148 Salt bridges: A:R.145 SO4.4: 3 residues within 4Å: Chain B: R.81, P.90, T.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.92 Salt bridges: B:R.81

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
C

B
D

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

Beta-2-microglobulin

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