SMTL ID : 1u3l.1

IspF with Mg and CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.63 Chain B: E.135 Ligands: CDP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.135, B:E.135 MG.4: 3 residues within 4Å: Chain B: D.63 Chain C: E.135 Ligands: CDP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.135, C:E.135 MG.7: 3 residues within 4Å: Chain A: E.135 Chain C: D.63 Ligands: CDP.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.135, A:E.135

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: CDP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:D.8, A:H.10, A:H.42 ZN.5: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: CDP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42 ZN.8: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: CDP.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42

3 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.3: 17 residues within 4Å: Chain A: D.8, H.10, H.42, D.56, G.58, D.63 Chain B: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: MG.1, ZN.2 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.131, B:T.133 Hydrogen bonds: B:A.100, B:M.105, B:L.106, B:T.132, B:T.133, A:D.56, A:G.58 Salt bridges: A:H.10, A:H.42 CDP.6: 17 residues within 4Å: Chain B: D.8, H.10, H.42, D.56, G.58, D.63 Chain C: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: MG.4, ZN.5 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.131, C:T.133 Hydrogen bonds: C:A.100, C:M.105, C:L.106, C:T.133, B:D.56, B:G.58 Salt bridges: B:H.10, B:H.42 CDP.9: 17 residues within 4Å: Chain A: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Chain C: D.8, H.10, H.42, D.56, G.58, D.63 Ligands: MG.7, ZN.8 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:D.56, C:G.58, A:A.100, A:M.105, A:L.106, A:T.132, A:T.133 Salt bridges: C:H.10, C:H.42 Hydrophobic interactions: A:A.131, A:T.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinbacher, S. et al., Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase Involved in Mevalonate Independent Biosynthesis of Isoprenoids. J.Mol.Biol. (2002)

Release Date

2004-08-31

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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