SMTL ID : 6m31.1

Structural and Functional Insights into an Archaeal Lipid Synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

LDA.1: 9 residues within 4Å: Chain A: T.22, A.23, I.25, G.26, I.29, T.144, V.147, F.148 Ligands: MPG.24 Ligand excluded by PLIP LDA.2: 4 residues within 4Å: Chain A: W.230 Chain B: L.42 Ligands: LDA.9, LDA.34 Ligand excluded by PLIP LDA.3: 4 residues within 4Å: Chain A: L.42 Chain B: W.230 Ligands: LDA.4, MPG.17 Ligand excluded by PLIP LDA.4: 5 residues within 4Å: Chain A: D.40, I.41, L.42 Ligands: LDA.3, MPG.17 Ligand excluded by PLIP LDA.5: 6 residues within 4Å: Chain A: V.17, I.21 Ligands: MPG.19, MPG.25, MPG.26, LDA.38 Ligand excluded by PLIP LDA.6: 3 residues within 4Å: Chain A: I.233, I.237, L.241 Ligand excluded by PLIP LDA.7: 9 residues within 4Å: Chain A: Y.57, L.97, L.101, V.102, L.112, V.116, A.119, L.120, Y.123 Ligand excluded by PLIP LDA.8: 3 residues within 4Å: Chain A: Y.110 Ligands: LDA.11, MPG.28 Ligand excluded by PLIP LDA.9: 4 residues within 4Å: Chain A: W.230, V.278 Ligands: LDA.2, LDA.34 Ligand excluded by PLIP LDA.10: 5 residues within 4Å: Chain A: K.90, A.94, I.95, I.98 Ligands: MPG.16 Ligand excluded by PLIP LDA.11: 6 residues within 4Å: Chain A: K.156, N.157, V.158, M.159 Ligands: LDA.8, MPG.28 Ligand excluded by PLIP LDA.29: 10 residues within 4Å: Chain B: Y.110, L.149, V.153, G.155, K.156, V.158, V.162, F.165, L.166 Ligands: LDA.37 Ligand excluded by PLIP LDA.30: 10 residues within 4Å: Chain B: K.18, I.21, T.22, A.23, I.25, G.26, T.144, V.147 Ligands: LDA.38, MPG.48 Ligand excluded by PLIP LDA.31: 9 residues within 4Å: Chain B: Y.57, L.97, L.101, L.105, L.112, A.119, L.120, Y.123 Ligands: MPG.44 Ligand excluded by PLIP LDA.32: 6 residues within 4Å: Chain B: L.8, V.17, K.18, I.21 Ligands: MPG.45, MPG.47 Ligand excluded by PLIP LDA.33: 4 residues within 4Å: Chain A: M.5 Chain B: L.241, F.264 Ligands: LDA.36 Ligand excluded by PLIP LDA.34: 5 residues within 4Å: Chain B: D.40, I.41, L.42 Ligands: LDA.2, LDA.9 Ligand excluded by PLIP LDA.35: 7 residues within 4Å: Chain A: L.274 Chain B: I.28, I.39, L.45, F.48, F.49 Ligands: MPG.47 Ligand excluded by PLIP LDA.36: 7 residues within 4Å: Chain A: M.5 Chain B: I.237, F.264, I.267, I.271 Ligands: MPG.19, LDA.33 Ligand excluded by PLIP LDA.37: 6 residues within 4Å: Chain B: K.156, N.157, V.158, M.159, V.162 Ligands: LDA.29 Ligand excluded by PLIP LDA.38: 7 residues within 4Å: Chain B: K.266, N.270 Ligands: LDA.5, MPG.26, MPG.27, LDA.30, MPG.47 Ligand excluded by PLIP LDA.39: 2 residues within 4Å: Chain B: L.224, K.225 Ligand excluded by PLIP LDA.40: 5 residues within 4Å: Chain B: K.91, A.94, I.95, I.98 Ligands: PO4.42 Ligand excluded by PLIP

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

PO4.12: 3 residues within 4Å: Chain A: R.16, K.74, R.77 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.16, A:K.74, A:R.77 PO4.13: 4 residues within 4Å: Chain A: R.175, K.179, K.266 Ligands: MPG.23 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.175, A:K.179, A:K.266 PO4.14: 5 residues within 4Å: Chain A: N.62, D.66, D.70, K.74, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.62, A:D.66, A:D.66 Salt bridges: A:K.74, A:K.130 PO4.41: 3 residues within 4Å: Chain B: R.16, K.74, R.77 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.16, B:K.74, B:R.77 PO4.42: 3 residues within 4Å: Chain B: N.87, K.91 Ligands: LDA.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.87 Water bridges: B:K.85 Salt bridges: B:K.91

2 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 6 residues within 4Å: Chain A: D.63, D.66, I.67, D.70, L.79, P.80 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.63, A:D.70, H2O.1 MG.43: 6 residues within 4Å: Chain B: D.63, D.66, I.67, D.70, L.79, P.80 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.63, B:D.70, H2O.2

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

MPG.16: 5 residues within 4Å: Chain A: L.105, F.106, I.107 Ligands: LDA.10, MPG.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.105, A:F.106, A:F.106 Hydrogen bonds: A:I.107 MPG.17: 9 residues within 4Å: Chain A: K.43, L.45, L.46, L.103, F.106 Ligands: LDA.3, LDA.4, MPG.16, MPG.26 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.45, A:L.46, A:L.46, A:L.103 MPG.18: 5 residues within 4Å: Chain A: Y.205, F.206, F.209 Ligands: MPG.21, MPG.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.205, A:F.206, A:F.209, A:F.209 MPG.19: 12 residues within 4Å: Chain A: L.8, K.9, L.12, E.13, R.16, V.17, K.18, N.19 Chain B: I.271 Ligands: LDA.5, MPG.25, LDA.36 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.8, A:K.9, A:L.12, A:L.12, A:V.17, B:I.271 Hydrogen bonds: A:R.16, A:K.18, A:N.19 Salt bridges: A:K.18 MPG.20: 7 residues within 4Å: Chain A: Y.222, L.232, A.236, I.240, I.243, Y.244 Ligands: MPG.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.222, A:L.232, A:A.236, A:I.243, A:I.243, A:I.243 MPG.21: 3 residues within 4Å: Chain A: Y.205 Ligands: MPG.18, MPG.20 No protein-ligand interaction detected (PLIP) MPG.22: 3 residues within 4Å: Chain A: I.223, L.224 Ligands: MPG.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.224 MPG.23: 20 residues within 4Å: Chain A: I.140, F.148, L.164, C.167, S.168, S.171, I.172, R.175, E.176, K.179, A.214, V.215, S.218, D.239, F.242, M.269, N.270, V.272 Ligands: PO4.13, MPG.24 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.148, A:L.164, A:I.172, A:A.214, A:V.215, A:F.242 Water bridges: A:R.175 Salt bridges: A:R.175, A:K.179 MPG.24: 17 residues within 4Å: Chain A: R.16, V.51, V.54, C.55, N.59, N.62, I.114, A.115, N.118, L.122, Y.125, L.143, T.144, V.147, F.150 Ligands: LDA.1, MPG.23 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.51, A:V.51, A:V.54, A:I.114, A:L.122, A:L.122, A:Y.125, A:L.143, A:L.143, A:V.147, A:F.150, A:F.150 Hydrogen bonds: A:R.16, A:N.62 Salt bridges: A:K.130 MPG.25: 12 residues within 4Å: Chain A: I.28, I.39, I.41, S.44, L.45, F.48, F.49 Chain B: I.267, N.270 Ligands: LDA.5, MPG.19, MPG.26 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.267, B:N.270, A:F.48, A:F.49 MPG.26: 13 residues within 4Å: Chain A: Y.11, F.48, F.52, F.53, E.88, K.91, F.92, I.95, L.99 Ligands: LDA.5, MPG.17, MPG.25, LDA.38 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.48, A:F.52, A:F.52, A:F.52, A:F.53, A:I.95, A:L.99 Hydrogen bonds: A:E.88 MPG.27: 4 residues within 4Å: Chain A: I.28, N.270 Ligands: LDA.38, MPG.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.28 MPG.28: 8 residues within 4Å: Chain A: N.108, Y.110, V.153, G.155, K.156, V.158 Ligands: LDA.8, LDA.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.110, A:V.153 Hydrogen bonds: A:N.108, A:V.153, A:K.156, A:V.158 MPG.44: 4 residues within 4Å: Chain B: L.105, N.108, I.109 Ligands: LDA.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.105, B:I.109 Hydrogen bonds: B:I.109 MPG.45: 10 residues within 4Å: Chain A: I.267, I.271 Chain B: K.9, L.12, E.13, R.16, V.17, K.18, N.19 Ligands: LDA.32 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.9, B:L.12, B:L.12, B:L.12, B:V.17, A:I.267, A:I.271 Hydrogen bonds: B:K.18, B:N.19 Salt bridges: B:K.18 MPG.46: 13 residues within 4Å: Chain B: F.148, C.167, S.168, S.171, I.172, R.175, E.176, K.179, A.214, F.242, K.266, M.269, V.272 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.148, B:I.172, B:I.172, B:A.214, B:F.242, B:M.269 Salt bridges: B:R.175, B:K.179, B:K.266 MPG.47: 11 residues within 4Å: Chain B: I.25, I.28, I.29, L.32, N.270, L.273, I.277 Ligands: MPG.27, LDA.32, LDA.35, LDA.38 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.25, B:I.28, B:I.29, B:L.32, B:N.270, B:L.273, B:I.277 MPG.48: 15 residues within 4Å: Chain B: R.16, V.51, V.54, C.55, N.59, N.62, I.114, A.115, N.118, L.122, L.143, T.144, V.147, F.150 Ligands: LDA.30 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.51, B:V.51, B:V.54, B:I.114, B:L.122, B:L.122, B:L.143, B:L.143, B:F.150, B:F.150 Salt bridges: B:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, S. et al., Structural and Functional Insights into an Archaeal Lipid Synthase. Cell Rep (2020)

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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