SMTL ID : 1u40.1

IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: CDM.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:D.8, A:H.10, A:H.42 ZN.3: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: CDM.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42 ZN.5: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: CDM.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42

3 x CDM: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL(Non-covalent)

CDM.2: 26 residues within 4Å: Chain A: D.8, H.10, H.34, S.35, H.42, D.56, I.57, G.58, K.59, F.61, P.62, D.63, F.68, L.76 Chain B: A.100, Q.101, A.102, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: ZN.1 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.57, A:L.76, B:T.133 Hydrogen bonds: A:H.34, A:D.56, A:I.57, A:G.58, A:D.63, A:D.63, B:A.100, B:M.105, B:L.106, B:T.132, B:T.133, B:E.135 Salt bridges: A:H.10, A:H.42 CDM.4: 26 residues within 4Å: Chain B: D.8, H.10, H.34, S.35, H.42, D.56, I.57, G.58, K.59, F.61, P.62, D.63, F.68, L.76 Chain C: A.100, Q.101, A.102, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: ZN.3 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.57, B:L.76, C:T.133 Hydrogen bonds: B:H.34, B:D.56, B:I.57, B:G.58, B:D.63, B:D.63, C:A.100, C:M.105, C:L.106, C:T.133, C:E.135 Salt bridges: B:H.10, B:H.42 CDM.6: 26 residues within 4Å: Chain A: A.100, Q.101, A.102, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Chain C: D.8, H.10, H.34, S.35, H.42, D.56, I.57, G.58, K.59, F.61, P.62, D.63, F.68, L.76 Ligands: ZN.5 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:I.57, C:L.76, A:T.133 Hydrogen bonds: C:H.34, C:D.56, C:I.57, C:G.58, C:D.63, C:D.63, A:A.100, A:M.105, A:L.106, A:T.132, A:T.133 Salt bridges: C:H.10, C:H.42

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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