SMTL ID : 4no5.1

Crystal structure of non-phosphorylated form of AMPD2 phosphopeptide bound to HLA-A2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLN- ILE- SER- GLN- ASP- VAL- LYS- LEU: AMP deaminase 2(Non-covalent)

ARG-GLN-ILE-SER-GLN-ASP-VAL-LYS-LEU.1: 26 residues within 4Å: Chain A: M.5, Y.7, M.45, E.63, K.66, V.67, A.69, 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, Q.155, L.156, Y.159, T.163, W.167, Y.171 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.7, A:D.77, A:Y.99, A:Y.116, A:Y.116, A:W.147, A:V.152, A:L.156, A:Y.159, A:Y.159, A:Y.159, A:T.163, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:V.67, A:D.77, A:Y.99, A:Y.99, A:Y.116, A:T.143, A:V.152, A:Y.159, A:Y.171 Water bridges: A:E.63, A:R.65, A:T.80, A:R.97, A:W.147 Salt bridges: A:K.146

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: S.195, H.197, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.195, A:H.197, A:E.198 EDO.4: 9 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.9, S.10, H.12, P.13, M.98 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.10, B:H.12 Water bridges: A:Q.242 EDO.5: 5 residues within 4Å: Chain A: Y.27, P.235 Chain B: S.51, Y.62, L.64 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.51, B:S.51 Water bridges: A:Y.27

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: R.14, P.15, G.16, R.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14, A:G.16, A:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohammed, F. et al., The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status. Oncotarget (2017)

Release Date

2014-12-24

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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