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

Structure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-trimer

Ligands

3 x 79N: (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate(Non-covalent)

79N.1: 9 residues within 4Å: Chain A: W.27, R.31, W.34, L.48, V.51, M.72, M.75 Chain B: I.119 Ligands: 79M.4 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.119, A:W.27, A:W.34, A:W.34, A:L.48, A:V.51 Hydrogen bonds: A:R.31 79N.2: 6 residues within 4Å: Chain A: V.52, I.53, W.56, L.57, F.129 Ligands: 79N.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.52, A:I.53, A:W.56, A:W.56, A:W.56, A:W.56, A:W.56, A:L.57 79N.3: 3 residues within 4Å: Chain A: L.49, W.56 Ligands: 79N.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.49

6 x 79M: (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate(Non-covalent)

79M.4: 5 residues within 4Å: Chain A: A.55, R.64 Chain B: I.119 Ligands: 79N.1, 79M.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.119 79M.5: 8 residues within 4Å: Chain A: A.61, R.64 Chain B: V.118, A.122, I.123, W.126, S.127 Ligands: 79M.4 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.64, A:R.64, B:S.127 Hydrophobic interactions: B:A.122, B:W.126, B:W.126, B:W.126 79M.6: 9 residues within 4Å: Chain B: A.55, V.59, A.61, R.64 Chain C: I.119, A.122, I.123, W.126, S.127 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:A.55, C:I.119, C:A.122, C:I.123, C:I.123, C:W.126 Hydrogen bonds: B:R.64 Water bridges: B:A.61 79M.7: 10 residues within 4Å: Chain B: E.43, A.46, C.50, V.71, V.74, E.78, A.117, W.121, L.125, F.129 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.117, B:W.121, B:W.121, B:W.121, B:W.121, B:L.125, B:F.129, B:F.129 Hydrogen bonds: B:E.78 79M.8: 4 residues within 4Å: Chain B: I.53, W.56, L.57, D.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.58 79M.9: 1 residues within 4Å: Chain C: W.126 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase. Nat.Commun. (2015)

Release Date

2015-09-30

Peptides

DIACYLGLYCEROL KINASE-DELTA 7: 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.
Show / Hide

DIACYLGLYCEROL KINASE-DELTA 7

Related Entries With Identical Sequence