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SMTL ID : 7kgq.1

Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LEU- LEU- LEU- ASP- ARG- LEU- ASN- GLN- LEU: Nucleoprotein(Non-covalent)

LEU-LEU-LEU-ASP-ARG-LEU-ASN-GLN-LEU.1:

30 residues within 4Å:

Chain A: M.5, Y.7, F.9, M.45, Y.59, E.63, R.65, K.66, V.67, H.70, V.76, D.77, T.80, L.81, Y.84, R.97, Y.99, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171
Ligands: EDO.6

37 PLIP interactions:

37 interactions with chain A

Hydrophobic interactions: A:Y.7, A:F.9, A:Y.59, A:V.67, A:D.77, A:L.81, A:Y.99, A:Y.116, A:T.143, A:W.147, A:V.152, A:L.156, A:Y.159, A:Y.159, A:T.163, A:W.167
Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:D.77, A:Y.99, A:Y.99, A:K.146, A:Q.155, A:Y.159, A:Y.171
Water bridges: A:R.65, A:K.66, A:T.73, A:T.73, A:D.77, A:T.80, A:R.97, A:Q.155, A:Q.155
Salt bridges: A:R.65, A:K.146

2 x CD: CADMIUM ION(Non-covalent)

CD.2:	1 residues within 4Å: Chain A: H.191 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.191, A:H.191, H₂O.12
CD.3:	3 residues within 4Å: Chain A: H.197, E.198 Ligands: CA.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.197, A:E.198, H₂O.3

2 x CA: CALCIUM ION(Non-covalent)

CA.4:	2 residues within 4Å: Chain A: E.198 Ligands: CD.3 No protein-ligand interaction detected (PLIP)
CA.5:	3 residues within 4Å: Chain B: N.83, H.84, L.87 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.84, B:L.87, H₂O.20

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6:

7 residues within 4Å:

Chain A: R.97, H.114, W.147, V.152, L.156
Ligands: LEU-LEU-LEU-ASP-ARG-LEU-ASN-GLN-LEU.1, LEU-LEU-LEU-ASP-ARG-LEU-ASN-GLN-LEU.1

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:R.97, A:R.97

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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