SMTL ID : 1knj.1

Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: CDI.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:D.8, A:H.10, A:H.42 MN.4: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: CDI.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42 MN.7: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: CDI.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42

3 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 12 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.56, G.58 Ligands: CDI.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.131, A:T.133 Hydrogen bonds: A:A.100, A:K.104, A:L.106, A:A.131, A:T.132, A:T.133, A:E.135, A:E.135, C:D.56, C:G.58 C5P.5: 12 residues within 4Å: Chain A: D.56, G.58 Chain B: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: CDI.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.131, B:T.133 Hydrogen bonds: B:A.100, B:K.104, B:L.106, B:A.131, B:T.133, B:E.135, B:E.135, A:D.56, A:G.58 C5P.8: 12 residues within 4Å: Chain B: D.56, G.58 Chain C: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: CDI.9 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:D.56, B:G.58, C:A.100, C:K.104, C:L.106, C:A.131, C:T.132, C:T.133, C:E.135 Hydrophobic interactions: C:A.131, C:T.133

3 x CDI: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE(Non-covalent)

CDI.3: 10 residues within 4Å: Chain C: D.8, H.10, A.33, H.34, S.35, H.42, I.57, P.62 Ligands: C5P.2, MN.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.34, C:H.34, C:S.35 Salt bridges: C:H.10, C:H.10, C:H.42, C:H.42 CDI.6: 10 residues within 4Å: Chain A: D.8, H.10, A.33, H.34, S.35, H.42, I.57, P.62 Ligands: MN.1, C5P.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.34, A:H.34, A:S.35 Salt bridges: A:H.10, A:H.10, A:H.42, A:H.42 CDI.9: 10 residues within 4Å: Chain B: D.8, H.10, A.33, H.34, S.35, H.42, I.57, P.62 Ligands: MN.4, C5P.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.34, B:H.34, B:S.35 Salt bridges: B:H.10, B:H.10, B:H.42, B:H.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richard, S.B. et al., Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway. J.Biol.Chem. (2002)

Release Date

2002-06-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

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

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