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SMTL ID : 6o4y.1

Structure of HLA-A2:01 with peptide MM91

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- LEU- VAL- VAL- GLY- ALA- VAL- GLY- VAL: Peptide MM91(Non-covalent)

LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1:

26 residues within 4Å:

Chain A: M.5, Y.7, F.9, M.45, Y.59, E.63, K.66, V.67, H.70, T.73, D.77, T.80, L.81, Y.84, R.97, Y.99, Y.116, T.143, K.146, W.147, V.152, Y.159, W.167, Y.171
Ligands: NA.6, GOL.8

31 PLIP interactions:

31 interactions with chain A

Hydrophobic interactions: A:Y.7, A:F.9, A:Y.59, A:K.66, A:V.67, A:T.73, A:D.77, A:L.81, A:Y.99, A:Y.116, A:T.143, A:W.147, A:V.152, A:Y.159, A:W.167, A:W.167
Hydrogen bonds: A:E.63, A:D.77, A:Y.84, A:Y.99, A:Y.99, A:T.143, A:K.146, A:Y.159, A:Y.171
Water bridges: A:K.66, A:K.66, A:K.66, A:K.66, A:D.77
Salt bridges: A:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.63, A:R.6, A:R.6, A:D.30 Water bridges: B:Y.63
GOL.7:	9 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14, M.99 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.11 Water bridges: A:H.188, A:Q.242, B:R.12, B:D.98
GOL.8:	10 residues within 4Å: Chain A: R.97, H.114, W.147, V.152, L.156 Ligands: LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:R.97

4 x NA: SODIUM ION(Non-functional Binders)

NA.3:	6 residues within 4Å: Chain A: D.37, A.40, S.42, Q.43, R.44 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.37, A:A.40, A:Q.43
NA.4:	6 residues within 4Å: Chain A: F.36, D.37, S.42, R.44, E.46 Ligands: NA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.35, A:D.37, A:D.37, A:E.46
NA.5:	7 residues within 4Å: Chain A: T.94, V.95, Q.96, A.117, Y.118, D.119, G.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.96, A:Q.96, A:G.120
NA.6:	9 residues within 4Å: Chain A: T.73, D.77, R.97, Y.116, W.147 Ligands: LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, LYS-LEU-VAL-VAL-GLY-ALA-VAL-GLY-VAL.1, GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.77, A:R.97, A:R.97

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Mishto, M. et al., Anin silico-in vitroPipeline Identifying an HLA-A*02:01+KRAS G12V+Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients. Front Immunol (2019)

Release Date

2020-01-15

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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