SMTL ID : 4s39.1

IspG in complex with HMBPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.297, P.298, G.299, C.300, R.302, T.303, M.341, G.342, C.343, V.345 Ligands: H6P.7 6 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions, Salt bridges: B:E.232, B:E.232 Metal complexes: A:C.297, A:C.300, A:C.343, H2O.1 SF4.6: 11 residues within 4Å: Chain B: C.297, P.298, G.299, C.300, R.302, T.303, M.341, G.342, C.343, V.345 Ligands: H6P.2 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:C.297, B:C.300, B:C.343, H2O.18 Salt bridges: A:E.232, A:E.232

2 x H6P: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate(Non-covalent)

H6P.2: 15 residues within 4Å: Chain A: M.29, R.56, D.87, H.89, R.110, N.112, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Chain B: N.346 Ligands: SF4.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.110, A:R.110, A:N.112, A:T.231, A:E.232, A:S.262 Water bridges: A:R.141, A:K.204, A:K.204, A:R.260, A:S.262 Salt bridges: A:R.56, A:R.56, A:R.110, A:R.141, A:K.204, A:K.204, A:R.260 H6P.7: 15 residues within 4Å: Chain A: N.346 Chain B: M.29, R.56, D.87, H.89, R.110, N.112, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Ligands: SF4.1 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.110, B:R.110, B:N.112, B:E.232, B:S.262 Water bridges: B:R.141, B:K.204, B:K.204, B:R.260, B:S.262 Salt bridges: B:R.56, B:R.56, B:R.110, B:R.141, B:K.204, B:K.204, B:R.260

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: T.155, M.158, D.159 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: E.276, Q.279, E.280, Q.283, F.290, A.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.276, A:Q.283, A:A.291 Water bridges: A:E.293 GOL.5: 9 residues within 4Å: Chain A: N.31, P.265, A.266, G.268, E.269, P.270, R.271 Chain B: S.305, Q.309 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.31, A:N.31, A:A.266, A:G.268, B:Q.309 Water bridges: A:Q.43, B:S.305 GOL.8: 3 residues within 4Å: Chain B: T.155, M.158, D.159 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain B: E.276, Q.279, E.280, Q.283, F.290, A.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.276, B:Q.283, B:A.291 GOL.10: 9 residues within 4Å: Chain A: S.305, Q.309 Chain B: N.31, P.265, A.266, G.268, E.269, P.270, R.271 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.309, B:N.31, B:N.31, B:A.266, B:G.268 Water bridges: A:S.305, B:Q.43

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

2015-04-29

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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