SMTL ID : 6wzy.1

Structure of DbNA(10) peptides bound to H-2Db MHC-I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: G.113, Y.114, L.115, Q.116, L.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.113, A:L.115, A:Q.116 EDO.3: 5 residues within 4Å: Chain A: V.232, R.235 Chain B: Q.8, V.9, M.99 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.235, B:V.9, B:V.9

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

PEG.2: 6 residues within 4Å: Chain A: Q.73, W.74, R.76, V.77 Chain C: A.7, A.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76 Water bridges: A:W.74 PEG.4: 6 residues within 4Å: Chain A: R.7, F.9, Y.28, N.31 Chain B: F.56, Y.63 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.31, B:F.56, B:F.56, B:Y.63 Water bridges: A:S.5, A:R.7, A:Y.28

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain B: R.45, E.47, K.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.48 Water bridges: B:V.49 Salt bridges: B:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Assmus, L.M. et al., Overlapping Peptides Elicit Distinct CD8 + T Cell Responses following Influenza A Virus Infection. J Immunol. (2020)

Release Date

2020-09-16

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B
Epitope from Neuraminidase Protein (NA-181-190): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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

Beta-2-microglobulin

Epitope from Neuraminidase Protein (NA-181-190)

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