SMTL ID : 3fqt.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 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- LEU- LEU- GLY- SER- PRO- VAL- ARG- ALA: peptide 38-46 from cell division cycle 25b (CDC25b): GLLGSPVRA(Non-covalent)

GLY-LEU-LEU-GLY-SER-PRO-VAL-ARG-ALA.1: 25 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, A.69, H.70, T.73, V.76, D.77, T.80, Y.84, R.97, Y.99, T.143, K.146, W.147, V.152, L.156, Y.159, W.167, Y.171 Ligands: GOL.14 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.7, A:F.9, A:K.66, A:V.67, A:V.76, A:Y.99, A:T.143, A:V.152, A:L.156, A:Y.159, A:Y.159 Hydrogen bonds: A:E.63, A:T.73, A:T.73, A:D.77, A:Y.84, A:Y.99, A:T.143, A:Y.171, A:Y.171 Water bridges: A:K.66, A:K.66, A:D.77, A:R.97 Salt bridges: A:K.146

6 x CD: CADMIUM ION(Non-covalent)

CD.2: 1 residues within 4Å: Chain A: H.145 No protein-ligand interaction detected (PLIP) CD.3: 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.1 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:E.212, A:E.212, H2O.1, H2O.8, H2O.9 CD.5: 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.11, H2O.12 CD.6: 2 residues within 4Å: Chain A: E.148, E.154 No protein-ligand interaction detected (PLIP) CD.12: 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.7, H2O.15, H2O.15, H2O.15

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: E.19, Q.72 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.19, A:E.19, H2O.3

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: P.57, D.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.61, A:D.61 GOL.9: 4 residues within 4Å: Chain A: T.163, E.166, W.167, R.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170 GOL.10: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.6, A:R.6 Water bridges: A:Y.27, A:D.30 GOL.11: 6 residues within 4Å: Chain A: E.58, Y.59, G.62, E.63, K.66, W.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.59, A:E.63, A:K.66, A:K.66 GOL.13: 6 residues within 4Å: Chain A: R.21, I.23 Chain B: S.32, D.33, H.50, L.63 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.33, B:D.33, A:R.14 Water bridges: B:S.32, B:I.34, B:H.50, A:R.21 GOL.14: 8 residues within 4Å: Chain A: R.97, H.114, W.147, V.152, L.156 Ligands: GLY-LEU-LEU-GLY-SER-PRO-VAL-ARG-ALA.1, GLY-LEU-LEU-GLY-SER-PRO-VAL-ARG-ALA.1, GLY-LEU-LEU-GLY-SER-PRO-VAL-ARG-ALA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:R.97

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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