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SMTL ID : 8elg.1

Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANAF from OC43 virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- GLN- LYS- LEU- ILE- ALA- ASN- ALA- PHE: NQK-OC43 peptide(Non-covalent)

ASN-GLN-LYS-LEU-ILE-ALA-ASN-ALA-PHE.1:

29 residues within 4Å:

Chain A: M.5, Y.7, Y.9, M.45, R.62, E.63, I.66, S.67, N.70, T.73, E.76, S.77, N.80, Y.84, R.97, Y.99, S.116, Y.123, T.143, K.146, W.147, A.150, E.152, Q.155, W.156, Y.159, L.163, W.167, Y.171

36 PLIP interactions:

36 interactions with chain A

Hydrophobic interactions: A:Y.7, A:Y.9, A:I.66, A:I.66, A:E.76, A:Y.123, A:Y.123, A:E.152, A:W.156, A:Y.159, A:Y.159, A:Y.159, A:W.167
Hydrogen bonds: A:Y.7, A:Y.9, A:Y.9, A:R.62, A:R.62, A:R.62, A:E.63, A:N.70, A:N.70, A:T.73, A:S.77, A:N.80, A:Y.84, A:Y.99, A:E.152, A:Y.171
Water bridges: A:Y.7, A:E.63, A:E.76, A:S.77, A:Q.155
Salt bridges: A:K.146
pi-Stacking: A:W.147

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2:	1 residues within 4Å: Chain A: D.119 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.119 Salt bridges: A:H.93
ACT.3:	8 residues within 4Å: Chain A: H.3, L.179, Q.180, R.181, A.182, Y.209, P.210, E.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181 Water bridges: A:D.29 Salt bridges: A:H.3
ACT.4:	8 residues within 4Å: Chain A: W.204, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14, R.97 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.204 Hydrogen bonds: A:Q.242, B:S.11 Salt bridges: A:R.234 Water bridges: B:M.99

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Augusto, D.G. et al., A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature (2023)

Release Date

2023-06-14

Peptides

heavy chain HLA-B*15:01: 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

heavy chain HLA-B*15:01

Beta-2-microglobulin

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