SMTL ID : 6iie.1

Crystal structure of human diacylglycerol kinase alpha EF-hand domains bound to Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.19, D.21, N.23, I.25, E.30 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.19, A:I.25, A:E.30, A:E.30, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.64, D.66, S.68, S.70, E.75 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.64, A:D.66, A:S.68, A:E.75, A:E.75

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: G.80, A.81, T.82, T.83, V.84, P.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.80, A:T.83 GOL.4: 4 residues within 4Å: Chain A: Q.37, R.40, Y.44 Ligands: PG4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37, A:Q.37

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 1 residues within 4Å: Chain A: W.47 No protein-ligand interaction detected (PLIP) PG4.6: 5 residues within 4Å: Chain A: Y.44, G.91, L.92, E.93 Ligands: GOL.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, D. et al., Crystal structure and calcium-induced conformational changes of diacylglycerol kinase alpha EF-hand domains. Protein Sci. (2019)

Release Date

2019-02-20

Peptides

Diacylglycerol kinase alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diacylglycerol kinase alpha