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

Diacylglycerol Kinase solved by multi crystal multi orientation native SAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

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

78N.1: 13 residues within 4Å: Chain A: N.81, S.107, V.110, L.111, I.114, V.118, I.119 Chain B: I.19, A.22, A.23, S.26 Ligands: 78N.2, 78N.7 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.111, A:I.114, A:I.114, A:I.119, B:I.19 Hydrogen bonds: A:N.81, A:S.107, A:L.111, B:S.26 78N.2: 11 residues within 4Å: Chain A: E.43, A.46, V.71, V.74, E.78, A.117, W.121, A.122 Chain B: I.19 Ligands: 78N.1, 78N.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.46, A:V.74, A:A.117, A:W.121 Hydrogen bonds: A:E.43, A:E.78 78N.3: 6 residues within 4Å: Chain A: A.55, R.64 Chain C: I.119, I.123, W.126, S.127 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Salt bridges: A:R.64 Hydrophobic interactions: C:I.119, C:I.123, C:W.126 Hydrogen bonds: C:S.127 78N.5: 10 residues within 4Å: Chain A: I.112 Chain B: W.27, L.30, R.31, W.34, I.35, L.48, M.72, M.75 Ligands: 78N.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.27, B:L.30, B:L.30, B:W.34, B:W.34, A:I.112 Salt bridges: B:R.31 78N.6: 6 residues within 4Å: Chain A: I.123 Chain B: V.51, A.55, R.64 Ligands: 78N.5, 78N.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.64 Salt bridges: B:R.64 Hydrophobic interactions: A:I.123 78N.7: 11 residues within 4Å: Chain A: V.118, A.122, I.123, W.126 Chain B: V.59, D.60, A.61, R.64 Ligands: 78N.1, 78N.2, 78N.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.64, B:R.64, B:R.64 Hydrophobic interactions: A:V.118, A:A.122, A:W.126, A:W.126 78N.10: 9 residues within 4Å: Chain C: A.46, C.50, I.53, V.74, E.78, I.114, A.117, W.121, L.125 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.46, C:I.53, C:W.121, C:W.121, C:L.125

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

78M.4: 4 residues within 4Å: Chain A: I.53, W.56, L.57, D.58 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.53, A:L.57 Hydrogen bonds: A:D.58 78M.8: 5 residues within 4Å: Chain B: C.50, I.53, L.57, W.121, F.129 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.121

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

NA.9: 4 residues within 4Å: Chain A: L.73, D.116 Chain B: S.69, L.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olieric, V. et al., Data-collection strategy for challenging native SAD phasing. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-03-23

Peptides

Diacylglycerol kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Membrane

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

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