SMTL ID : 4brb.1 (1 other biounit)

Crystal structure of the integral membrane enzyme DgkA-ref, delta 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

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

78N.1: 7 residues within 4Å: Chain A: Q.42, E.43, C.50, V.71, I.114, A.117, W.121 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.43, A:V.71, A:I.114, A:A.117, A:W.121 Hydrogen bonds: A:Q.42 78N.2: 10 residues within 4Å: Chain A: L.30, R.31, W.34, I.35, V.47, L.48, M.72, M.75 Ligands: 78N.3, 78N.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.34, A:V.47, A:L.48 Hydrogen bonds: A:R.31 Salt bridges: A:R.31 78N.3: 4 residues within 4Å: Chain A: W.34, L.48, L.49 Ligands: 78N.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.34 78N.4: 8 residues within 4Å: Chain A: V.51, A.55, L.57, R.64 Chain B: I.119, I.123 Ligands: 78N.2, 78N.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.51, B:I.119, B:I.123 Hydrogen bonds: A:W.56, A:R.64, A:R.64 Salt bridges: A:R.64 78N.5: 4 residues within 4Å: Chain B: I.119, I.123, W.126 Ligands: 78N.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.119, B:I.123, B:W.126, B:W.126, B:W.126 78N.6: 7 residues within 4Å: Chain B: A.55, A.61, R.64 Chain C: I.119, I.123, W.126, S.127 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.55, C:I.119, C:W.126 Hydrogen bonds: B:R.64, C:I.123 Salt bridges: B:R.64 78N.7: 8 residues within 4Å: Chain A: R.18 Chain B: Q.42, E.43, A.46, E.78, I.114, A.117, W.121 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.43, B:E.43, B:A.46, B:A.117, B:W.121, B:W.121 Hydrogen bonds: B:E.43 78N.8: 7 residues within 4Å: Chain A: D.116, I.119 Chain C: V.51, A.55, D.58, R.64, M.72 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.51, A:I.119 Hydrogen bonds: C:D.58, C:D.58 Salt bridges: C:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic. Sci.Rep. (2014)

Release Date

2014-06-18

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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