SMTL ID : 3q1o.1 (2 other biounits)

Crystal structure of geranyltransferase from helicobacter pylori complexed with magnesium and isoprenyl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.101, D.107, R.112 Ligands: DMA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.101, A:D.107, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.101, D.107, R.112 Ligands: DMA.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.101, B:D.107, H2O.4, H2O.4

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.2: 11 residues within 4Å: Chain A: G.55, K.56, R.59, H.94, L.98, R.113, T.196, F.233, Q.234, D.237 Ligands: DMA.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.98, A:T.196, A:F.233 Hydrogen bonds: A:K.56 Water bridges: A:K.56, A:R.57, A:R.59, A:R.59, A:R.112, A:K.251 Salt bridges: A:K.56, A:K.56, A:R.59, A:H.94, A:H.94, A:R.113 DMA.3: 14 residues within 4Å: Chain A: S.97, L.98, D.101, D.107, R.112, M.168, Q.172, K.195, Q.234, D.237, K.251, K.259 Ligands: MG.1, DMA.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.98, A:D.101, A:K.195 Hydrogen bonds: A:Q.234, A:D.237, A:D.237 Water bridges: A:R.112, A:Q.172, A:Q.172, A:K.195, A:D.238, A:K.251 Salt bridges: A:R.112, A:K.195, A:K.251, A:K.259 DMA.8: 11 residues within 4Å: Chain B: G.55, K.56, R.59, H.94, L.98, R.113, T.196, F.233, Q.234, D.237 Ligands: DMA.9 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.98, B:T.196, B:F.233 Hydrogen bonds: B:K.56 Water bridges: B:K.56, B:R.57, B:R.59, B:R.59, B:K.251 Salt bridges: B:K.56, B:K.56, B:R.59, B:H.94, B:H.94, B:R.113 DMA.9: 14 residues within 4Å: Chain B: S.97, L.98, D.101, D.107, R.112, M.168, Q.172, K.195, Q.234, D.237, K.251, K.259 Ligands: MG.7, DMA.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.98, B:D.101, B:K.195 Hydrogen bonds: B:Q.234, B:D.237 Water bridges: B:D.107, B:D.107, B:D.107, B:Q.172, B:D.175, B:K.195, B:D.238, B:K.251 Salt bridges: B:R.112, B:K.195, B:K.251, B:K.259

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

SO4.4: 2 residues within 4Å: Chain A: E.148, S.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.149 SO4.5: 2 residues within 4Å: Chain A: N.20, R.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20 Salt bridges: A:R.24 SO4.6: 3 residues within 4Å: Chain A: S.27, K.30, N.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:N.31 Salt bridges: A:K.30 SO4.10: 2 residues within 4Å: Chain B: E.148, S.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.149 SO4.11: 2 residues within 4Å: Chain B: N.20, R.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.20 Salt bridges: B:R.24 SO4.12: 3 residues within 4Å: Chain B: S.27, K.30, N.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.31, B:N.31 Salt bridges: B:K.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallrapp, F.H. et al., Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2011-01-12

Peptides

Geranyltranstransferase (IspA): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Geranyltranstransferase (IspA)

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