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SMTL ID : 5gsd.1

Crystal structure of LMP2 peptide from EBV in complex with HLA-A*11:01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SER- SER- CYS- PRO- LEU- SER- LYS: Epstein Barr Virus, Latent membrane protein-2 epitope(Non-covalent)

SER-SER-CYS-PRO-LEU-SER-LYS.1:

18 residues within 4Å:

Chain A: Y.7, Y.9, E.63, N.66, A.69, Q.70, T.73, D.77, Y.84, I.95, Y.99, D.116, T.143, K.146, W.147, Q.155, Q.156, Y.159

16 PLIP interactions:

16 interactions with chain A

Hydrophobic interactions: A:A.69, A:T.143, A:W.147, A:W.147
Hydrogen bonds: A:Y.7, A:N.66, A:D.77, A:Y.99, A:D.116, A:Q.155, A:Q.156
Water bridges: A:Q.70, A:D.77, A:D.77, A:R.114, A:R.114

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	2 residues within 4Å: Chain A: H.188, M.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.189 Water bridges: A:T.187
GOL.3:	6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.63, A:D.30, A:D.30
GOL.4:	4 residues within 4Å: Chain A: M.45, P.47, E.53, W.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.45, A:E.53
GOL.5:	3 residues within 4Å: Chain B: N.83, H.84, V.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.83 Water bridges: B:H.84, B:V.85
GOL.6:	8 residues within 4Å: Chain B: I.7, Q.8, V.9, V.93, K.94, W.95, D.96, M.99 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.7, B:V.9, B:K.94, B:D.96 Water bridges: B:M.99

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xiao, Z. et al., Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens. Sci Rep (2017)

Release Date

2017-08-09

Peptides

HLA class I histocompatibility antigen, A-11 alpha chain: 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

HLA class I histocompatibility antigen, A-11 alpha chain

Beta-2-microglobulin

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