SMTL ID : 5d57.1 (1 other biounit)

In meso 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

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

78M.1: 4 residues within 4Å: Chain A: A.55, W.56, D.58 Ligands: 78M.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.56, A:W.56, A:W.56 Hydrogen bonds: A:D.58 Salt bridges: A:R.64 78M.2: 5 residues within 4Å: Chain A: A.46, C.50, I.53, L.57, F.129 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.46, A:I.53 78M.3: 5 residues within 4Å: Chain A: R.101, D.104, L.105, I.112 Chain C: L.79 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.79, C:L.79, A:I.112 Hydrogen bonds: A:R.101, A:R.101 78M.4: 12 residues within 4Å: Chain A: W.27, L.30, R.31, W.34, V.47, L.48, V.51, M.72, M.75 Chain B: I.112, I.119 Ligands: 78M.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.30, A:W.34, A:V.47, A:L.48, A:V.51, B:I.112, B:I.119 78M.5: 8 residues within 4Å: Chain A: A.55, R.64 Chain B: I.115, I.119 Ligands: 78M.1, 78M.4, 78M.6, 78M.7 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.115, B:I.119, A:A.55 Water bridges: A:R.64, A:R.64, A:R.64 Salt bridges: A:R.64 78M.6: 13 residues within 4Å: Chain A: I.19, A.22, A.23, S.26 Chain B: E.78, S.107, V.110, L.111, I.114, I.115 Ligands: 78M.5, 78M.7, 78M.8 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.114, B:I.115, A:I.19 Hydrogen bonds: B:E.78, B:S.107, B:L.111 78M.7: 5 residues within 4Å: Chain B: I.123, W.126 Ligands: 78M.5, 78M.6, 78M.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.126 78M.8: 14 residues within 4Å: Chain A: R.18, A.22 Chain B: E.43, A.46, V.47, V.71, V.74, E.78, I.114, A.117, W.121, A.122 Ligands: 78M.6, 78M.7 10 PLIP interactions: 8 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, B:W.121, B:A.122 Hydrogen bonds: A:R.18 Salt bridges: A:R.18 78M.9: 5 residues within 4Å: Chain B: A.55, R.64 Chain C: I.119, I.123, W.126 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Water bridges: B:R.64, B:R.64 Salt bridges: B:R.64 Hydrophobic interactions: C:I.119, C:I.123, C:W.126 78M.10: 3 residues within 4Å: Chain B: W.56, L.57, D.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.57 Hydrogen bonds: B:D.58 78M.11: 6 residues within 4Å: Chain C: A.46, L.49, C.50, I.53, I.114 Ligands: 78M.12 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.46, C:L.49, C:I.53, C:I.53 78M.12: 7 residues within 4Å: Chain C: E.43, V.71, M.75, E.78, W.121, L.125 Ligands: 78M.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.71, C:W.121, C:W.121, C:W.121, C:L.125

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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