SMTL ID : 5dwk.2 (1 other biounit)

Diacylglycerol Kinase solved by multi crystal multi orientation native SAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

4 x 78M: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78M.1: 5 residues within 4Å: Chain A: A.55, W.56, L.57, R.64, I.68 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.55, A:I.68 Hydrogen bonds: A:W.56, A:R.64 Salt bridges: A:R.64 78M.2: 5 residues within 4Å: Chain A: W.34, A.38, R.41, Q.42, V.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.34 78M.3: 8 residues within 4Å: Chain A: L.30, R.31, W.34, I.35, F.40, G.44, V.47, M.72 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.30, A:W.34, A:W.34, A:W.34, A:W.34, A:F.40, A:V.47 Hydrogen bonds: A:R.31, A:R.31 Salt bridges: A:R.31 78M.4: 4 residues within 4Å: Chain A: W.56, L.57, D.58, F.129 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.56, A:L.57 Hydrogen bonds: A:D.58

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: E.37, E.85 Ligands: CIT.6, ACT.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.37, A:E.37, A:E.85, A:E.85, ACT.7

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 2 residues within 4Å: Chain A: E.85 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.36

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: E.37, A.39, E.78, N.81, E.85 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olieric, V. et al., Data-collection strategy for challenging native SAD phasing. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-03-23

Peptides

Diacylglycerol kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
F

Membrane

We predict this structure to be a membrane protein.
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Diacylglycerol kinase

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