SMTL ID : 6m34.1

Structural and functional insights into an Archaeal synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

4 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.1: 4 residues within 4Å: Chain A: F.264, I.267, I.271 Chain B: M.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.264, A:I.267 MPG.4: 3 residues within 4Å: Chain A: W.230 Chain B: L.42 Ligands: MPG.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.42, A:W.230, A:W.230 MPG.7: 1 residues within 4Å: Chain B: F.264 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.264 MPG.9: 8 residues within 4Å: Chain B: L.42, L.45, L.46, F.53, L.99, L.103, F.106 Ligands: MPG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.42, B:L.45, B:L.46, B:F.53, B:F.53, B:L.99, B:L.99, B:L.103

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.2: 11 residues within 4Å: Chain A: T.144, L.164, S.168, S.171, I.172, K.266, M.269, N.270, V.272, L.273 Ligands: MG.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.164, A:M.269, A:V.272 DMA.3: 7 residues within 4Å: Chain A: R.16, G.58, N.59, N.62, Y.125, I.140, T.144 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.140 Hydrogen bonds: A:G.58, A:N.59, A:N.62 Salt bridges: A:R.16

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain A: R.175, K.179, K.266 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.175, A:K.179, A:K.266 PO4.10: 4 residues within 4Å: Chain B: R.175, K.179, K.266 Ligands: LDA.8 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.175, B:K.179, B:K.266

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: E.176 Ligands: DMA.2 No protein-ligand interaction detected (PLIP)

1 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.8: 8 residues within 4Å: Chain B: I.140, F.148, S.168, E.176, K.179, M.269, V.272 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.148, B:M.269, B:V.272 Hydrogen bonds: B:K.179 Salt bridges: B:E.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, C. et al., Structural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes. To Be Published

Release Date

2021-02-03

Peptides

Digeranylgeranylglyceryl phosphate synthase: 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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Digeranylgeranylglyceryl phosphate synthase

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