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SMTL ID : 3c9n.1

Crystal Structure of a SARS Corona Virus Derived Peptide Bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- GLN- GLN- GLU- SER- SER- PHE- VAL- MET: Peptide antigen(Non-covalent)

VAL-GLN-GLN-GLU-SER-SER-PHE-VAL-MET.1:

32 residues within 4Å:

Chain A: M.5, Y.7, Y.9, M.45, Y.59, R.62, E.63, I.66, S.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, L.95, R.97, Y.99, S.116, T.143, K.146, W.147, A.150, E.152, Q.155, W.156, Y.159, W.167, Y.171
Ligands: PG4.2

37 PLIP interactions:

37 interactions with chain A

Hydrophobic interactions: A:Y.7, A:Y.59, A:E.76, A:L.81, A:Y.99, A:T.143, A:A.150, A:E.152, A:W.156, A:Y.159, A:W.167, A:W.167
Hydrogen bonds: A:Y.9, A:R.62, A:R.62, A:E.63, A:E.63, A:N.70, A:N.70, A:S.77, A:N.80, A:Y.84, A:Y.99, A:E.152, A:W.156, A:Y.171, A:Y.171
Water bridges: A:Q.65, A:T.69, A:R.97, A:R.97, A:R.97, A:Y.99, A:Q.155, A:Y.159
Salt bridges: A:R.62, A:K.146

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2:

5 residues within 4Å:

Chain A: Y.59, R.62, L.163, W.167
Ligands: VAL-GLN-GLN-GLU-SER-SER-PHE-VAL-MET.1

1 PLIP interactions:

1 interactions with chain A

Water bridges: A:R.170

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3:

9 residues within 4Å:

Chain A: A.211, T.233, R.234, P.235, F.241
Chain B: Y.26, S.57, K.58, Y.63

7 PLIP interactions:

6 interactions with chain B, 1 interactions with chain A

Hydrogen bonds: B:K.58, A:T.233
Water bridges: B:Y.26, B:Y.26, B:D.59
Salt bridges: B:K.58
pi-Cation interactions: B:Y.63

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Roder, G. et al., Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501. ACTA CRYSTALLOGR.,SECT.F (2008)

Release Date

2008-02-26

Peptides

HLA class I histocompatibility antigen, B-15 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, B-15 alpha chain

Beta-2-microglobulin

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