SMTL ID : 1kbg.1

MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLY- TYR- VAL- TYR- ESC- GLY- LEU: PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)(Non-covalent)

ARG-GLY-TYR-VAL-TYR-ESC-GLY-LEU.1: 24 residues within 4Å: Chain A: Y.7, V.9, R.62, E.63, K.66, N.70, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, T.143, K.146, W.147, E.152, R.155, L.156, Y.159, W.167, Y.171 Ligands: GAL-GLA.3 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:V.9, A:K.66, A:F.74, A:D.77, A:L.81, A:Y.116, A:T.143, A:W.147, A:L.156, A:Y.159, A:Y.159, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:R.62, A:E.63, A:K.66, A:N.70, A:N.70, A:D.77, A:S.99, A:S.99, A:E.152, A:R.155, A:R.155, A:W.167, A:Y.171, A:Y.171 Water bridges: A:R.62, A:R.62, A:S.73, A:D.77, A:T.80 Salt bridges: A:K.146

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: Q.54, K.173, N.174, N.176, A.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.54, A:N.174, A:N.176

1 x GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose(Non-covalent)

GAL-GLA.3: 5 residues within 4Å: Chain A: A.150, G.151, E.152, R.155 Ligands: ARG-GLY-TYR-VAL-TYR-ESC-GLY-LEU.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.155

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 1 residues within 4Å: Chain A: N.86 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Speir, J.A. et al., Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL. Immunity (1999)

Release Date

1999-02-09

Peptides

PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB): A
PROTEIN (BETA-2-MICROGLOBULIN): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)

PROTEIN (BETA-2-MICROGLOBULIN)

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