SMTL ID : 5guf.1

Structural insight into an intramembrane enzyme for archaeal membrane lipids biosynthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 16 residues within 4Å: Chain A: P.31, V.32, G.35, G.56, K.57, T.58, G.61, L.62, D.100, S.104, K.107, R.108, R.114, G.115 Ligands: MG.2, K.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.31, A:K.57 Hydrogen bonds: A:T.58, A:T.58, A:R.114, A:R.114, A:G.115 Water bridges: A:N.28, A:G.56, A:D.100, A:S.104, A:S.104, A:K.107, A:K.107 Salt bridges: A:K.57, A:K.57, A:K.57, A:K.107, A:K.107, A:R.108, A:R.114 CTP.6: 16 residues within 4Å: Chain B: P.31, V.32, G.35, G.56, K.57, T.58, G.61, L.62, D.100, S.104, K.107, R.108, R.114, G.115 Ligands: MG.7, K.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.31, B:K.57 Hydrogen bonds: B:T.58, B:T.58, B:R.114, B:R.114, B:G.115 Water bridges: B:N.28, B:G.56, B:D.100, B:S.104, B:S.104, B:K.107, B:K.107 Salt bridges: B:K.57, B:K.57, B:K.57, B:K.107, B:K.107, B:R.108, B:R.114

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: CTP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.8, R.10, D.12, E.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:D.8, A:R.10, A:E.16, H2O.1 MG.4: 3 residues within 4Å: Chain A: R.50, R.51, R.108 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: CTP.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.8, R.10, D.12, E.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:D.8, B:R.10, B:E.16, H2O.4 MG.9: 3 residues within 4Å: Chain B: R.50, R.51, R.108 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: D.100, D.122, D.125 Ligands: CTP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, H2O.1, H2O.1 K.10: 4 residues within 4Å: Chain B: D.100, D.122, D.125 Ligands: CTP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, S. et al., Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Res. (2017)

Release Date

2017-10-11

Peptides

CDP-archaeol synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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CDP-archaeol synthase