SMTL ID : 5d56.2 (1 other biounit)

In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.37, E.85 Ligands: FLC.2, ACT.3 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.3

1 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 2 residues within 4Å: Chain A: E.85 Ligands: ZN.1 No protein-ligand interaction detected (PLIP)

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

ACT.3: 6 residues within 4Å: Chain A: E.37, A.39, E.78, S.82, E.85 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.39 Hydrogen bonds: A:E.78

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

78M.4: 4 residues within 4Å: Chain A: A.38, R.41, Q.42, V.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.45 78M.5: 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:F.129 Hydrogen bonds: A:D.58 78M.6: 9 residues within 4Å: Chain A: L.30, R.31, W.34, I.35, V.51, M.72 Chain B: I.112, I.115, I.119 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.30, A:W.34, A:V.51, B:I.112, B:I.115, B:I.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.Y. et al., In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-01-13

Peptides

Diacylglycerol kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Membrane

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

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