SMTL ID : 4uxz.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 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.4, ACT.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.37, A:E.37, A:E.85, A:E.85

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

79N.2: 5 residues within 4Å: Chain A: L.49, W.56, L.57, D.58, F.129 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.49, A:W.56, A:L.57, A:F.129, A:F.129 Hydrogen bonds: A:W.56

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

79M.3: 4 residues within 4Å: Chain A: R.31, W.34, I.35, L.48 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:W.34, A:W.34, A:W.34, A:L.48 Hydrogen bonds: A:W.34 Salt bridges: A:R.31

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 4 residues within 4Å: Chain A: E.37, E.85 Ligands: ZN.1, ACT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.85

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

ACT.5: 8 residues within 4Å: Chain A: E.37, A.39, E.78, N.81, S.82, E.85 Ligands: ZN.1, FLC.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.39 Hydrogen bonds: A:N.81

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
D

B
E

C
F

Membrane

We predict this structure to be a membrane protein.
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DIACYLGLYCEROL KINASE-DELTA 7

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