SMTL ID : 7cpn.1 (2 other biounits)

CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: T.191, E.192, A.193 Chain B: R.130, A.170 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.130, B:R.130, A:E.192, A:A.193

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 9 residues within 4Å: Chain A: M.43, D.44, G.45, N.46, G.47, R.48, R.57, H.61, R.95 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.45, A:N.46, A:N.46, A:G.47 Water bridges: A:R.48, A:R.57 Salt bridges: A:R.57, A:H.61, A:R.95 SO4.3: 8 residues within 4Å: Chain B: D.44, G.45, N.46, G.47, R.48, R.57, H.61, R.95 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.45, B:N.46, B:N.46, B:G.47 Water bridges: B:R.48, B:H.61, B:H.61 Salt bridges: B:R.57, B:H.61, B:R.95 SO4.4: 7 residues within 4Å: Chain A: Y.229, R.260, Y.261, G.262 Chain B: R.212, R.218, S.220 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.262, B:S.220, B:S.220 Water bridges: A:Y.229, A:R.260, A:Y.261 Salt bridges: B:R.212, B:R.218 SO4.5: 5 residues within 4Å: Chain B: R.112, R.115, K.140, E.141, E.144 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.112, B:R.115 SO4.6: 2 residues within 4Å: Chain B: H.119, H.151 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.151, B:H.151 Salt bridges: B:H.119, B:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kurokawa, H. et al., Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-10-14

Peptides

Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific)

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