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SMTL ID : 7kgo.1

Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ILE- LEU- LEU- ASN- LYS- HIS- ILE- ASP- ALA: Nucleoprotein(Non-covalent)

ILE-LEU-LEU-ASN-LYS-HIS-ILE-ASP-ALA.1:

24 residues within 4Å:

Chain A: M.5, Y.7, F.9, M.45, E.63, R.65, K.66, V.67, H.70, T.73, D.77, T.80, Y.84, R.97, Y.99, T.143, K.146, W.147, V.152, L.156, Y.159, T.163, W.167, Y.171

30 PLIP interactions:

30 interactions with chain A

Hydrophobic interactions: A:Y.7, A:Y.7, A:F.9, A:K.66, A:V.67, A:V.152, A:L.156, A:Y.159, A:T.163, A:W.167, A:W.167, A:W.167
Hydrogen bonds: A:E.63, A:R.65, A:R.65, A:D.77, A:Y.84, A:Y.99, A:Y.99, A:H.114, A:T.143, A:K.146, A:Y.171, A:Y.171
Water bridges: A:D.77, A:R.97, A:R.97
Salt bridges: A:K.146, A:K.146
pi-Stacking: A:H.70

3 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.2:	3 residues within 4Å: Chain A: R.14, G.16, R.17 No protein-ligand interaction detected (PLIP)
3NI.3:	2 residues within 4Å: Chain A: H.151, E.154 No protein-ligand interaction detected (PLIP)
3NI.7:	4 residues within 4Å: Chain B: N.42, G.43, E.77, A.79 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4:	3 residues within 4Å: Chain A: W.51, E.177, T.178 Ligand excluded by PLIP
CL.5:	2 residues within 4Å: Chain A: H.191, W.274 Ligand excluded by PLIP
CL.8:	3 residues within 4Å: Chain B: T.73, E.74, K.75 Ligand excluded by PLIP

1 x CD: CADMIUM ION(Non-covalent)

CD.6:

2 residues within 4Å:

Chain A: H.151, E.154

2 PLIP interactions:

2 interactions with chain A

Metal complexes: A:H.151, A:E.154

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Szeto, C. et al., The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule. Iscience (2021)

Release Date

2021-01-20

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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