5grg.1 | SWISS-MODEL Template Library

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SMTL ID : 5grg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-mer

Ligands

2 x SER- SER- CYS- SER- SER- CYS: Epstein Barr Virus, Latent Membrane Protein 2 epitope(Non-covalent)

SER-SER-CYS-SER-SER-CYS.1:	14 residues within 4Å: Chain A: M.5, Y.7, Y.9, E.63, N.66, Q.70, Y.99, R.114, Q.155, Y.159, R.163, W.167, Y.171 Ligands: PRO-LEU-SER-LYS.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.63, A:E.63, A:N.66, A:Y.99, A:R.114, A:Q.155, A:Y.159, A:R.163, A:R.163, A:Y.171 Water bridges: A:Q.62, A:E.63
SER-SER-CYS-SER-SER-CYS.2:	12 residues within 4Å: Chain A: D.77, T.80, L.81, Y.84, I.95, D.116, T.143, K.146, W.147, A.152, Q.156 Ligands: SER-SER-CYS-SER-SER-CYS.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.81, A:T.143, A:A.152 Hydrogen bonds: A:D.77, A:D.116, A:T.143 Water bridges: A:D.77, A:D.77 Salt bridges: A:K.146

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:	5 residues within 4Å: Chain A: R.6, F.8, D.29, D.30 Chain B: Y.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.30
GOL.4:	3 residues within 4Å: Chain A: H.188, M.189, W.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.189
GOL.5:	4 residues within 4Å: Chain B: D.34, N.83, H.84, V.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.34 Water bridges: B:H.84, B:V.85
GOL.6:	6 residues within 4Å: Chain A: R.21 Chain B: S.33, D.34, I.35, H.51, Y.66 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.33, B:I.35, B:Y.66, A:R.21 Water bridges: B:H.51, B:Y.66

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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