SMTL ID : 4s3c.1

IspG in complex with Epoxide Intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x 43Q: (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate(Non-covalent)

43Q.1: 15 residues within 4Å: Chain A: V.345, N.346 Chain B: M.29, R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Ligands: SF4.2 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:H.89, B:R.110, B:R.110, B:N.145, B:E.232, B:S.262 Water bridges: B:R.141, B:K.204, B:K.204, B:K.204, B:R.260 Salt bridges: B:R.56, B:R.56, B:R.110, B:R.141, B:K.204, B:K.204, B:R.260 43Q.4: 15 residues within 4Å: Chain A: M.29, R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Chain B: V.345, N.346 Ligands: SF4.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:H.89, A:R.110, A:R.110, A:N.145, A:T.231, A:E.232, A:S.262 Water bridges: A:R.141, A:K.204, A:K.204, A:K.204, A:R.260 Salt bridges: A:R.56, A:R.56, A:R.110, A:R.141, A:K.204, A:K.204, A:R.260

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 10 residues within 4Å: Chain A: C.297, P.298, G.299, C.300, R.302, T.303, G.342, C.343, V.345 Ligands: 43Q.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.297, A:C.300, A:C.343 Salt bridges: B:E.232, B:E.232 SF4.5: 10 residues within 4Å: Chain B: C.297, P.298, G.299, C.300, R.302, T.303, G.342, C.343, V.345 Ligands: 43Q.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, Salt bridges: A:E.232, A:E.232 Metal complexes: B:C.297, B:C.300, B:C.343

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.276, Q.279, E.280, Q.283, F.290, A.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.279, A:Q.283, A:A.291 Water bridges: A:Q.283, A:E.293 GOL.6: 6 residues within 4Å: Chain B: E.276, Q.279, E.280, Q.283, F.290, A.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.279, B:Q.283, B:A.291 Water bridges: B:Q.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quitterer, F. et al., Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE). J.Mol.Biol. (2015)

Release Date

2015-05-06

Peptides

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase

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