SMTL ID : 3fqr.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-1-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.62 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.6, A:R.6, A:D.30, B:Y.62 Water bridges: B:Y.62 GOL.7: 8 residues within 4Å: Chain A: R.14, R.21, I.23 Chain B: S.32, D.33, H.50, L.53, L.63 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.14, B:D.33 Water bridges: A:R.21, B:I.34, B:H.50 GOL.8: 7 residues within 4Å: Chain A: V.231, R.234, W.244 Chain B: Q.7, V.8, V.92, M.98 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.8, B:V.8, A:R.234

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: E.19 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.19, H2O.13 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.17, H2O.18

6 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: G.1, H.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.1, A:H.3, H2O.8, H2O.9 CD.4: 2 residues within 4Å: Chain A: D.30, E.212 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.30, A:E.212, H2O.1, H2O.2, H2O.11 CD.5: 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.5 CD.6: 2 residues within 4Å: Chain A: H.197, E.198 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.197, H2O.5 CD.10: 1 residues within 4Å: Chain B: H.50 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.50, H2O.14, H2O.16, H2O.17, H2O.19 CD.11: 3 residues within 4Å: Chain C: S.4, G.5, H.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.4, C:H.7

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
phospho-peptide 30-39 from beta-Catenin: YLD(Sep)GIHSGA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

phospho-peptide 30-39 from beta-Catenin: YLD(Sep)GIHSGA

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