SMTL ID : 4iho.1 (1 other biounit)

Crystal structure of H-2Db Y159F in complex with chimeric gp100

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- GLY- PRO- ARG- ASN- GLN- ASP- TRP- LEU: NONAMERIC PEPTIDE CHIMERIC GP100(Non-covalent)

GLU-GLY-PRO-ARG-ASN-GLN-ASP-TRP-LEU.1: 30 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.59, R.62, E.63, K.66, Q.70, W.73, F.74, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, Y.123, T.143, K.146, W.147, S.150, G.151, A.152, H.155, Y.156, F.159, W.167, Y.171 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.59, A:W.73, A:W.73, A:V.76, A:L.81, A:L.95, A:Y.123, A:W.147, A:F.159, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:Q.70, A:Q.70, A:Q.97, A:Q.97, A:T.143, A:S.150, A:S.150, A:S.150, A:Y.156, A:Y.171 Water bridges: A:W.73 Salt bridges: A:R.62, A:K.66, A:K.146, A:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.85, Y.118, E.119, R.121 No protein-ligand interaction detected (PLIP) GOL.3: 2 residues within 4Å: Chain A: R.21 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 GOL.5: 6 residues within 4Å: Chain A: R.21 Chain B: M.51, S.52, D.53, M.54 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.51, B:D.53, B:M.54, A:R.21, A:R.21

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

SO4.4: 1 residues within 4Å: Chain A: R.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uchtenhagen, H. et al., Proline substitution independently enhances H-2D(b) complex stabilization and TCR recognition of melanoma-associated peptides. Eur.J.Immunol. (2013)

Release Date

2013-09-11

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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