SMTL ID : 7p0a.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 PEPTIDE with D-AMINOACID (p3P6f)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- ALA- PRO- TYR- ASN- DPN- ALA- THR- MET: Stable signal peptide(Non-covalent)

LYS-ALA-PRO-TYR-ASN-DPN-ALA-THR-MET.1: 29 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.45, Y.59, R.62, E.63, K.66, Q.70, W.73, F.74, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, F.116, Y.123, T.143, W.147, S.150, H.155, Y.156, Y.159, E.163, W.167, Y.171 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:W.73, A:Y.159 Hydrogen bonds: A:Y.7, A:R.62, A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Q.97, A:Q.97, A:Y.156, A:Y.171, A:Y.171 Salt bridges: A:K.146 pi-Stacking: A:H.155

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

SO4.2: 4 residues within 4Å: Chain A: R.14, R.21, D.39 Chain B: H.36 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.39 Salt bridges: A:R.14, A:R.21, B:H.36 SO4.3: 3 residues within 4Å: Chain A: R.121 Chain B: I.3, K.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.5, A:R.121 SO4.4: 4 residues within 4Å: Chain A: P.15, G.16, A.89, G.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.16, A:G.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ballabio, F. et al., l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics. Acs Omega (2022)

Release Date

2022-03-23

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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