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SMTL ID : 4nnx.1

Crystal structure of PKD2 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- ALA- SEP- LEU- SER- ILE- SER- VAL: Serine/threonine-protein kinase D2(Non-covalent)

ARG-GLN-ALA-SEP-LEU-SER-ILE-SER-VAL.1:

27 residues within 4Å:

Chain A: M.5, Y.7, F.9, M.45, E.63, R.65, K.66, V.67, T.73, V.76, D.77, T.80, L.81, Y.84, R.97, Y.99, 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:L.81, A:T.143, A:V.152, A:L.156, A:Y.159, A:W.167
Hydrogen bonds: A:E.63, A:E.63, A:K.66, A:D.77, A:D.77, A:Y.84, A:Y.99, A:T.143, A:K.146, A:W.167, A:Y.171, A:Y.171
Water bridges: A:R.65, A:K.66, A:A.69, A:H.70, A:T.73, A:T.73, A:D.77, A:D.77, A:Y.99
Salt bridges: A:R.65, A:K.66, A:K.146

4 x CD: CADMIUM ION(Non-covalent)

CD.2:	2 residues within 4Å: Chain A: H.151, E.154 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.151, A:E.154, A:E.154
CD.3:	2 residues within 4Å: Chain A: D.30, E.212 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.30, A:D.30, A:E.212, H₂O.5, H₂O.5
CD.4:	1 residues within 4Å: Chain A: H.197 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.197
CD.6:	1 residues within 4Å: Chain B: H.51 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.51, H₂O.5, H₂O.8, H₂O.8

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

5 residues within 4Å:

Chain A: R.21, I.23
Chain B: S.33, D.34, H.51

4 PLIP interactions:

3 interactions with chain B, 1 interactions with chain A

Hydrogen bonds: B:D.34, B:D.34
Water bridges: B:H.51, A:R.21

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

2014-11-19

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

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