SMTL ID : 3ze3.1 (1 other biounit)

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.37, A:E.37, A:E.85, A:E.85

1 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 4 residues within 4Å: Chain A: E.37, E.85 Ligands: ZN.1, ACT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.85

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

ACT.3: 8 residues within 4Å: Chain A: E.37, A.39, E.78, N.81, S.82, E.85 Ligands: ZN.1, FLC.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.39 Hydrogen bonds: A:N.81

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

78M.4: 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.5: 5 residues within 4Å: Chain A: R.31, W.34, F.40, G.44, L.48 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:W.34, A:F.40, A:L.48 Hydrogen bonds: A:R.31 78M.6: 4 residues within 4Å: Chain A: L.111, I.114, V.118, A.122 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.114, A:V.118, A:V.118 78M.7: 4 residues within 4Å: Chain A: W.56, L.57, D.58, F.129 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.56, A:L.57, A:F.129 Hydrogen bonds: A:D.58

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: S.69 Chain B: S.70, D.116, T.120 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.116, A:S.69 Water bridges: A:S.69 NA.9: 4 residues within 4Å: Chain A: L.73, D.116 Chain C: S.69, L.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Crystal Structure of the Integral Membrane Diacylglycerol Kinase. Nature (2013)

Release Date

2013-05-22

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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