SMTL ID : 3tbv.1 (3 other biounits)

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (A2G,V3P,Y4A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- GLY- PRO- ALA- ASN- PHE- ALA- THR- MET: Glycoprotein G1(Non-covalent)

LYS-GLY-PRO-ALA-ASN-PHE-ALA-THR-MET.1: 26 residues within 4Å: Chain A: M.5, Y.7, E.9, R.62, E.63, K.66, Q.70, W.73, 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 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:E.63, A:W.73, A:W.73, A:H.155, A:Y.159, A:W.167, A:W.167 Hydrogen bonds: A:E.63, A:E.63, A:K.66, A:Q.70, A:Q.70, A:W.73, A:S.77, A:N.80, A:Q.97, A:T.143, A:Y.156, A:Y.159, A:Y.171 Water bridges: A:K.66, A:Y.156 Salt bridges: A:K.146 pi-Stacking: A:Y.156 pi-Cation interactions: A:H.155

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

SO4.2: 4 residues within 4Å: Chain A: P.15, A.89, G.90, G.91 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.90, A:G.91 Water bridges: A:P.15, A:G.16, A:L.17, A:S.88, A:G.91

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: F.8, E.9, T.10, I.23, V.25, Y.27, R.35 Chain B: M.54, S.55, F.56 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.55, B:F.56, A:T.10, A:I.23, A:Y.27, A:Y.27, A:R.35 GOL.4: 3 residues within 4Å: Chain A: R.144, R.145, E.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.148 GOL.5: 3 residues within 4Å: Chain B: Y.26, S.57, Y.63 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.26, B:S.57, B:Y.63 Water bridges: B:F.56, B:K.58, B:Y.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duru, A.D. et al., Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition. To be Published

Release Date

2012-08-08

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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