SMTL ID : 5d56.1 (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

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

78M.1: 11 residues within 4Å: Chain A: W.27, L.30, R.31, W.34, V.47, L.48, M.72, M.75 Chain B: I.115, I.119 Ligands: 78M.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.27, A:L.30, A:W.34, A:V.47, B:I.115, B:I.119 78M.2: 5 residues within 4Å: Chain A: A.55, R.64 Ligands: 78M.1, 78M.4, 78M.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 78M.3: 13 residues within 4Å: Chain A: R.18 Chain B: E.43, A.46, V.47, V.71, V.74, E.78, I.114, A.117, W.121, A.122 Ligands: 78M.4, 78M.6 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.46, B:V.47, B:V.71, B:V.74, B:A.117, B:W.121 Hydrogen bonds: A:R.18, A:R.18 78M.4: 13 residues within 4Å: Chain A: I.19, A.22, A.23, S.26 Chain B: N.81, S.107, V.110, L.111, I.114, V.118 Ligands: 78M.2, 78M.3, 78M.6 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.111, B:I.114, B:V.118, A:I.19 Hydrogen bonds: B:N.81, B:S.107 78M.5: 4 residues within 4Å: Chain B: I.53, W.56, L.57, D.58 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.53, B:L.57 Hydrogen bonds: B:D.58 78M.6: 6 residues within 4Å: Chain B: V.118, A.122, W.126 Ligands: 78M.2, 78M.3, 78M.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.118, B:A.122, B:W.126, B:W.126 78M.7: 7 residues within 4Å: Chain B: A.55, R.64 Chain C: V.118, I.119, A.122, I.123, W.126 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.118, C:I.119, C:A.122, C:I.123, C:W.126 Salt bridges: B:R.64 78M.8: 6 residues within 4Å: Chain C: E.43, I.53, V.74, M.75, E.78, W.121 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.53, C:V.74, C:W.121, C:W.121

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
A

B
B

C
C

Membrane

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

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