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SMTL ID : 1qlf.1

MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PHE- ALA- PRO- SER- ASN- TYR- PRO- ALA- LEU: SYNTHETIC GLYCOPEPTIDE(Non-covalent)

PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1:

31 residues within 4Å:

Chain A: M.5, Y.7, E.9, Y.45, Y.59, E.63, K.66, Q.70, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, F.116, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171
Ligands: NAG.5

32 PLIP interactions:

32 interactions with chain A

Hydrophobic interactions: A:Y.7, A:W.73, A:W.73, A:V.76, A:L.81, A:L.95, A:Y.123, A:W.147, A:W.147, A:A.152, A:H.155, A:Y.159, A:E.163, A:W.167, A:W.167
Hydrogen bonds: A:Y.7, A:E.63, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Y.84, A:Q.97, A:Q.97, A:K.146, A:Y.156, A:Y.156, A:Y.171
Salt bridges: A:K.146
pi-Stacking: A:H.155, A:W.167
pi-Cation interactions: A:K.66

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	3 residues within 4Å: Chain A: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.167, A:R.170, A:R.170
GOL.4:	5 residues within 4Å: Chain A: F.8, Y.27, N.30 Chain B: F.56, Y.63 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.30, A:N.30, B:F.56 Water bridges: A:N.30, B:Y.63

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

SO4.3:

2 residues within 4Å:

Chain A: R.121
Chain B: I.1

3 PLIP interactions:

2 interactions with chain B, 1 interactions with chain A

Hydrogen bonds: B:I.1, B:I.1
Salt bridges: A:R.121

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.5:

3 residues within 4Å:

Ligands: PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Glithero, A. et al., Crystal Structures of Two H-2Db/Glycopeptide Complexes Suggest a Molecular Basis for Ctl Cross-Reactivity. Immunity (1999)

Release Date

1999-09-01

Peptides

MHC CLASS I H-2DB HEAVY CHAIN: A
HUMAN BETA-2-MICROGLOBULIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

MHC CLASS I H-2DB HEAVY CHAIN

HUMAN BETA-2-MICROGLOBULIN

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