SMTL ID : 1h48.1 (1 other biounit)

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

CDI.1: 14 residues within 4Å: Chain A: D.10, H.12, A.35, H.36, S.37, H.44, I.59, G.60, F.63, D.65, F.70 Chain B: E.137 Ligands: ZN.2, C5P.5 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.59 Hydrogen bonds: A:D.10, A:H.36, A:H.36, A:S.37, A:F.63, A:D.65, A:D.65, B:E.137 Salt bridges: A:H.12, A:H.12, A:H.44, A:H.44 CDI.6: 13 residues within 4Å: Chain B: D.10, H.12, A.35, H.36, S.37, H.44, I.59, F.63, D.65, F.70 Chain C: E.137 Ligands: ZN.7, C5P.8 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.36, B:H.36, B:S.37, B:F.63, B:F.70, C:E.137 Salt bridges: B:H.12, B:H.12, B:H.44, B:H.44 CDI.9: 16 residues within 4Å: Chain A: E.137 Chain C: D.10, H.12, A.35, H.36, S.37, H.44, I.59, G.60, F.63, P.64, D.65, F.70, L.78 Ligands: C5P.3, ZN.10 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain C Hydrogen bonds: A:E.137, C:H.36, C:H.36, C:S.37, C:F.63, C:P.64, C:D.65 Hydrophobic interactions: C:I.59, C:L.78 Salt bridges: C:H.12, C:H.12, C:H.44, C:H.44

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.10, H.12, H.44 Ligands: CDI.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.10, A:H.12, A:H.44 ZN.7: 4 residues within 4Å: Chain B: D.10, H.12, H.44 Ligands: CDI.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.10, B:H.12, B:H.44 ZN.10: 4 residues within 4Å: Chain C: D.10, H.12, H.44 Ligands: CDI.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.10, C:H.12, C:H.44

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

C5P.3: 14 residues within 4Å: Chain A: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Chain C: D.58, G.60, K.61, D.65 Ligands: CDI.9 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.133, A:T.135 Hydrogen bonds: A:A.102, A:K.106, A:M.107, A:L.108, A:A.133, A:T.134, A:T.135, A:E.137, A:E.137, C:D.10, C:D.58, C:G.60 C5P.5: 13 residues within 4Å: Chain A: D.58, G.60, D.65 Chain B: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Ligands: CDI.1 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.58, A:G.60, B:A.102, B:M.107, B:L.108, B:T.134, B:T.134, B:T.135, B:T.135 Hydrophobic interactions: B:A.133, B:T.135 C5P.8: 13 residues within 4Å: Chain B: D.58, G.60, D.65 Chain C: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Ligands: CDI.6 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.135 Hydrogen bonds: C:A.102, C:K.106, C:M.107, C:L.108, C:T.135, C:E.137, C:E.137, C:E.137, B:D.58, B:G.60 pi-Cation interactions: C:K.106

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

MN.4: 6 residues within 4Å: Chain A: H.7, E.151 Chain B: H.7, E.151 Chain C: H.7, E.151 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Metal complexes: A:E.151, A:E.151, B:E.151, C:E.151, C:E.151

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.11: 16 residues within 4Å: Chain A: F.9, I.101, G.140, F.141, T.142, R.144, E.151 Chain B: F.9, G.140, F.141, R.144 Chain C: F.9, G.140, F.141, R.144, E.151 16 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: A:I.101, A:F.141, A:T.142, C:F.9, C:F.9, C:F.141, B:F.9 Hydrogen bonds: A:F.141, C:F.141, B:F.141 Water bridges: A:R.144, A:R.144, B:R.144 Salt bridges: A:R.144, C:R.144, B:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kemp, L.E. et al., The Identification of Isoprenoids that Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase by Complementary Biophysical Methods. Acta Crystallogr.,Sect.D (2005)

Release Date

2004-12-22

Peptides

2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE

Related Entries With Identical Sequence