SMTL ID : 7p0a.2 (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

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: 24 residues within 4Å: Chain A: M.5, Y.7, M.52, E.55, E.63, Q.70, W.73, V.76, S.77, N.80, Y.84, Q.97, S.99, F.116, Y.123, I.124, T.143, K.146, W.147, H.155, Y.156, Y.159, W.167, Y.171 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.7, A:E.63, A:W.73, A:V.76, A:Y.159, A:W.167, A:W.167 Hydrogen bonds: A:E.55, A:E.63, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Q.97, A:Q.97, A:K.146, A:K.146, A:H.155, A:Y.171, A:Y.171 Salt bridges: A:K.146

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

SO4.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.3: 3 residues within 4Å: Chain A: P.15, A.89, G.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.90 Water bridges: A:G.91 SO4.4: 2 residues within 4Å: Chain B: K.50, V.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.50, B:V.51

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain B: I.3 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: K.5, T.6 Ligand excluded by PLIP

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
D

B
E

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

Beta-2-microglobulin

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