SMTL ID : 4zdq.1 (5 other biounits)

Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 19 residues within 4Å: Chain A: P.15, C.16, A.17, G.18, T.19, G.20, S.21, R.22, K.29, G.84, A.85, S.86, R.87, S.90, D.113, A.114, A.115, K.220 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.17, A:G.18, A:T.19, A:G.20, A:S.21, A:R.22, A:G.84, A:S.90, A:A.114, A:A.115 Water bridges: A:K.29 Salt bridges: A:R.22, A:R.22, A:K.29, A:K.29, A:K.220

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: CTP.1 No protein-ligand interaction detected (PLIP)

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 2 residues within 4Å: Chain A: D.48, G.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.48 ACT.4: 8 residues within 4Å: Chain A: R.87, D.113, R.116, A.170, Q.174, T.196, D.197, K.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.174 Water bridges: A:R.116 Salt bridges: A:R.87, A:R.116, A:K.220 ACT.5: 2 residues within 4Å: Chain A: V.79, R.80 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.80 ACT.6: 1 residues within 4Å: Chain A: D.146 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.169 ACT.7: 3 residues within 4Å: Chain A: D.228, E.231, A.232 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.231 Hydrogen bonds: A:E.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pierce, P.G. et al., Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis. Acta Crystallogr.,Sect.F (2024)

Release Date

2015-04-29

Peptides

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

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