SMTL ID : 4q2g.1

CRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL FOR PHOSPHOLIPID BIOSYNTHESIS (S200C/S223C, inactive mutant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

4 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 1 residues within 4Å: Chain A: C.220 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.220 HG.2: 3 residues within 4Å: Chain A: F.37, L.40, C.41 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.41 HG.5: 1 residues within 4Å: Chain B: C.220 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.220 HG.6: 3 residues within 4Å: Chain B: F.37, L.40, C.41 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:F.37, B:C.41

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.239, D.266, D.269 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.239, A:D.269, A:D.269 MG.7: 3 residues within 4Å: Chain B: D.239, D.266, D.269 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.239, B:D.266, B:D.269, B:D.269

2 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.4: 11 residues within 4Å: Chain A: V.34, V.38, L.51, V.52, I.55, F.141, L.157, W.161, D.164, R.267, L.271 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.38, A:L.51, A:V.52, A:I.55, A:F.141, A:F.141, A:L.157, A:L.271 Hydrogen bonds: A:D.164 Salt bridges: A:R.267 BNG.8: 8 residues within 4Å: Chain B: V.34, L.51, I.55, F.141, L.157, W.161, D.164, R.267 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.34, B:L.51, B:I.55, B:F.141 Hydrogen bonds: B:D.164 Salt bridges: B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis. Nat Commun (2014)

Release Date

2014-07-02

Peptides

Phosphatidate cytidylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Phosphatidate cytidylyltransferase