SMTL ID : 3fqx.1

Phosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted antigen presentation and generates tumor specific epitopes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- VAL- ALA- SEP- PRO- THR- SER- GLY- VAL: phospho-peptide 1097-1105 from insulin receptor substrate 2 (IRS2): RVA(Sep)PTSGV(Non-covalent)

ARG-VAL-ALA-SEP-PRO-THR-SER-GLY-VAL.1: 26 residues within 4Å: Chain A: M.5, Y.7, M.45, Y.59, E.63, K.66, A.69, H.70, T.73, D.77, T.80, L.81, Y.84, R.97, Y.99, H.114, Y.116, T.143, K.146, W.147, V.152, L.156, Y.159, T.163, W.167, Y.171 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:K.66, A:A.69, A:D.77, A:L.81, A:Y.99, A:Y.116, A:T.143, A:W.147, A:L.156, A:Y.159, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:D.77, A:R.97, A:R.97, A:Y.99, A:Y.99, A:K.146, A:Y.159, A:W.167, A:Y.171 Water bridges: A:K.66, A:K.66, A:D.77, A:T.80, A:K.146, A:K.146, A:K.146 Salt bridges: A:K.66, A:K.146

5 x CD: CADMIUM ION(Non-covalent)

CD.2: 2 residues within 4Å: Chain A: H.191, H.192 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.191, A:H.191 CD.3: 2 residues within 4Å: Chain A: G.1, H.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.1, A:H.3, H2O.5, H2O.6, H2O.8 CD.4: 1 residues within 4Å: Chain A: H.197 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.197, H2O.1, H2O.3, H2O.9, H2O.11 CD.5: 1 residues within 4Å: Chain A: D.30 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.30, A:D.30, H2O.3, H2O.6, H2O.6 CD.8: 1 residues within 4Å: Chain B: H.50 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.50, H2O.3, H2O.16

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: H.151, A.153, E.154 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: N.82, H.83, L.86 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.83, B:L.86, H2O.16, H2O.16

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.62 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.6, A:R.6, B:Y.62 Water bridges: A:D.30 GOL.10: 7 residues within 4Å: Chain A: R.21, I.23 Chain B: S.32, D.33, H.50, L.53, L.63 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.14, B:D.33 Water bridges: A:R.21, B:I.34, B:H.50, B:S.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petersen, J. et al., Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes. Proc.Natl.Acad.Sci.Usa (2009)

Release Date

2009-03-03

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

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