SMTL ID : 2v34.2 (1 other biounit)

IspE in complex with cytidine and ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.1: 8 residues within 4Å: Chain A: G.26, Y.27, H.28, K.148, T.174, G.175, Y.178 Ligands: SO4.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.27 Hydrogen bonds: A:H.28, A:H.28, A:H.28 Water bridges: A:G.26, A:T.174, A:S.179 pi-Stacking: A:Y.178

1 x SG3: [(1E,3R,4S)-4-FLUORO-3,5-DIHYDROXY-4-METHYLPENT-1-EN-1-YL]PHOSPHONIC ACID(Non-covalent)

SG3.2: 13 residues within 4Å: Chain A: K.12, P.91, P.92, G.93, G.95, L.96, G.97, G.98, G.99, D.133, T.174, G.240, S.241 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.174 Hydrogen bonds: A:K.12, A:K.12, A:P.91, A:G.93, A:A.94, A:G.95, A:G.97, A:G.98, A:G.99, A:S.241 Water bridges: A:K.88, A:K.88, A:P.91, A:L.96, A:L.96 Halogen bonds: A:S.241

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: E.208, N.209, F.237, V.238 Ligand excluded by PLIP

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.216, Y.226, R.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.226 Water bridges: A:R.216, A:R.216 Salt bridges: A:R.216, A:R.227 SO4.5: 4 residues within 4Å: Chain A: S.173, T.174, G.175 Ligands: CTN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:G.175 SO4.6: 2 residues within 4Å: Chain A: N.223, R.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.223 Water bridges: A:R.216 Salt bridges: A:R.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sgraja, T. et al., Characterization of Aquifex Aeolicus 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase -Ligand Recognition in a Template for Antimicrobial Drug Discovery. FEBS J. (2008)

Release Date

2007-06-26

Peptides

4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE

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