SMTL ID : 3vjc.1 (1 other biounit)

Crystal structure of the human squalene synthase in complex with zaragozic acid A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

3 x ZGA: Zaragozic acid A(Non-covalent)

ZGA.1: 21 residues within 4Å: Chain A: T.23, S.24, R.25, S.26, F.27, I.31, Y.46, R.50, D.53, K.90, M.123, V.148, V.152, L.184, N.188, R.191, F.261, M.268, A.269, T.272 Chain B: V.295 35 PLIP interactions: 34 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.27, A:I.31, A:Y.46, A:Y.46, A:Y.46, A:D.53, A:V.152, A:L.184, A:F.261, B:V.295 Hydrogen bonds: A:R.25, A:S.26, A:S.26, A:F.27, A:Y.46, A:Y.46, A:R.50, A:R.50 Water bridges: A:T.23, A:R.25, A:R.25, A:R.25, A:R.25, A:R.25, A:S.26, A:D.53, A:K.90, A:K.90, A:D.91 Salt bridges: A:R.25, A:R.25, A:R.50, A:K.90 pi-Stacking: A:F.27, A:Y.46 ZGA.3: 20 residues within 4Å: Chain B: T.23, S.24, R.25, S.26, F.27, Y.46, R.50, D.53, K.90, M.123, V.148, V.152, L.184, T.187, N.188, R.191, F.261, P.265, A.269, T.272 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.27, B:Y.46, B:Y.46, B:D.53, B:V.152, B:L.184, B:T.187, B:F.261, B:P.265 Hydrogen bonds: B:T.23, B:R.25, B:S.26, B:S.26, B:Y.46, B:Y.46, B:R.50, B:R.50 Water bridges: B:R.25, B:R.25, B:N.188 Salt bridges: B:R.25, B:R.25, B:R.50, B:K.90 pi-Stacking: B:F.27, B:Y.46 ZGA.6: 22 residues within 4Å: Chain C: T.23, S.24, R.25, S.26, F.27, I.31, Y.46, L.49, R.50, D.53, K.90, M.123, V.148, V.152, L.184, T.187, N.188, R.191, F.261, P.265, A.269, T.272 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:F.27, C:F.27, C:I.31, C:Y.46, C:Y.46, C:L.49, C:D.53, C:V.152, C:T.187, C:F.261, C:P.265, C:A.269 Hydrogen bonds: C:R.25, C:S.26, C:Y.46, C:Y.46, C:R.50, C:R.50, C:N.188 Water bridges: C:T.23, C:R.25, C:R.25, C:R.25, C:K.90, C:N.188, C:R.191 Salt bridges: C:R.25, C:R.25, C:R.50, C:K.90 pi-Stacking: C:F.27, C:Y.46

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

PO4.2: 4 residues within 4Å: Chain A: R.122, H.146, Y.147, L.151 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.121, A:R.121, A:R.122, A:Y.147 Salt bridges: A:R.122, A:H.146 PO4.4: 4 residues within 4Å: Chain B: R.122, H.146, Y.147, L.151 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.121, B:R.122, B:Y.147 Salt bridges: B:R.122, B:H.146 PO4.7: 3 residues within 4Å: Chain C: R.122, H.146, Y.147 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.122, C:R.122, C:R.122, C:R.122 Salt bridges: C:R.122, C:H.146

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain B: E.164 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C.I. et al., Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase. J.Biol.Chem. (2012)

Release Date

2012-04-11

Peptides

Squalene synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Squalene synthase

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