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SMTL ID : 6vb6.1

HLA-B*15:02 complexed with a synthetic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x THR- VAL- ARG- ALA- SER- GLY- HIS- SER- TYR: Synthetic peptide THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR(Non-covalent)

THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1:

31 residues within 4Å:

Chain A: Y.7, M.45, Y.59, R.62, N.63, I.66, T.69, N.70, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, I.95, R.97, Y.99, D.114, S.116, Y.123, T.143, K.146, W.147, A.150, E.152, L.156, Y.159, W.167, Y.171
Ligands: ACT.4

37 PLIP interactions:

37 interactions with chain A

Hydrophobic interactions: A:Y.7, A:I.66, A:Y.74, A:L.81, A:Y.99, A:Y.123, A:T.143, A:Y.159, A:Y.159, A:W.167
Hydrogen bonds: A:R.62, A:R.62, A:N.63, A:N.63, A:N.63, A:T.73, A:T.73, A:Y.74, A:E.76, A:S.77, A:N.80, A:Y.84, A:R.97, A:R.97, A:Y.99, A:S.116, A:S.116, A:E.152, A:Y.171, A:Y.171
Water bridges: A:N.70, A:Y.99, A:D.114
Salt bridges: A:D.114, A:K.146
pi-Stacking: A:W.147
pi-Cation interactions: A:Y.99

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	9 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, R.12, H.13, P.14 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.11, B:S.11 Water bridges: A:W.204
GOL.3:	6 residues within 4Å: Chain A: F.8, Y.27, D.29 Chain B: S.55, F.56, Y.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.55, B:F.56, B:Y.63, B:Y.63

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4:

8 residues within 4Å:

Chain A: Y.9, N.70, Y.74, R.97
Ligands: THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:Y.9, A:Y.74
Water bridges: A:N.70, A:N.70, A:R.97
Salt bridges: A:R.97

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Schutte, R.J. et al., HLA-B*15:02 complexed with a synthetic peptide. To Be Published

Release Date

2020-11-25

Peptides

MHC class I antigen: A
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 antigen

Beta-2-microglobulin

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