SMTL ID : 3ze3.2 (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

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

78N.1: 9 residues within 4Å: Chain A: W.27, R.31, W.34, I.35, L.48, M.72, M.75 Chain B: I.119 Ligands: 78N.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.27, A:W.34, A:W.34, A:L.48, B:I.119 Hydrogen bonds: A:R.31, A:R.31 78N.2: 7 residues within 4Å: Chain A: V.51, A.55, R.64 Chain B: I.119 Ligands: 78N.1, 78N.3, 78N.6 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.119, A:V.51, A:A.55 Water bridges: A:V.59, A:R.64 Salt bridges: A:R.64 78N.3: 10 residues within 4Å: Chain A: V.59, D.60, A.61, R.64 Chain B: A.122, I.123, W.126 Ligands: 78N.2, 78N.6, 78N.7 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.122, B:W.126, B:W.126 Hydrogen bonds: A:R.64, A:R.64 Water bridges: A:L.57, A:D.58 78N.6: 15 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, I.115, V.118, I.119 Ligands: 78N.2, 78N.3, 78N.7 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.111, B:I.114, B:I.115, B:V.118, B:I.119, A:I.19 Hydrogen bonds: B:N.81, B:S.107, B:L.111, A:S.26 78N.7: 10 residues within 4Å: Chain A: R.18 Chain B: E.43, V.71, V.74, E.78, A.117, W.121, A.122 Ligands: 78N.3, 78N.6 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.71, B:V.74, B:A.117, B:W.121 Hydrogen bonds: B:E.43, B:E.78, A:R.18, A:R.18 78N.8: 6 residues within 4Å: Chain B: A.55, R.64 Chain C: I.119, I.123, W.126, S.127 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.64 Water bridges: B:D.60, B:R.64 Salt bridges: B:R.64 Hydrophobic interactions: C:I.119, C:W.126 78N.9: 9 residues within 4Å: Chain C: E.43, I.53, V.71, V.74, E.78, A.117, V.118, W.121, L.125 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.53, C:V.71, C:W.121, C:W.121, C:W.121, C:L.125

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

78M.4: 2 residues within 4Å: Chain A: I.119, W.126 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.119 78M.5: 7 residues within 4Å: Chain A: A.46, C.50, I.53, L.57, W.121, L.125, F.129 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.46, A:I.53, A:W.121, A:L.125

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
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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