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SMTL ID : 8isn.1 (1 other biounit)

HLA-A24 in complex with modified 9mer WT1 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CYS- TYR- THR- TRP- ASN- GLN- MET- ASN- LEU: CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU(Non-covalent)

CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU.1:

28 residues within 4Å:

Chain A: M.5, Y.7, F.22, M.45, Y.59, E.63, K.66, V.67, H.70, T.73, E.76, N.77, I.80, Y.84, M.97, F.99, H.114, Y.123, T.143, K.146, W.147, V.152, Q.155, Q.156, Y.159, T.163, G.167, Y.171

25 PLIP interactions:

25 interactions with chain A

Hydrophobic interactions: A:K.66, A:N.77, A:I.80, A:I.80, A:F.99, A:Y.123, A:W.147
Hydrogen bonds: A:E.63, A:K.66, A:H.70, A:H.70, A:E.76, A:E.76, A:N.77, A:N.77, A:T.143, A:Q.156, A:Q.156, A:Y.171, A:Y.171
Water bridges: A:Y.59, A:H.70
Salt bridges: A:K.146
pi-Stacking: A:Y.7, A:F.99

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2:

1 residues within 4Å:

Chain A: N.86

No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:	7 residues within 4Å: Chain A: T.31, T.178, R.181, D.183, Y.209, G.239, T.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.31, A:R.181
GOL.4:	5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.63
GOL.5:	3 residues within 4Å: Chain A: S.88, A.90, G.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88, A:S.88
GOL.6:	4 residues within 4Å: Chain B: D.34, N.83, H.84, V.85 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.34, B:N.83 Water bridges: B:N.83, B:H.84, B:V.85
GOL.7:	3 residues within 4Å: Chain B: G.43, E.44, R.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.43, B:R.45

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bekker, G.J. et al., Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Sci. (2023)

Release Date

2023-09-13

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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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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Extreme

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