SMTL ID : 3q80.1

Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) Complexed with CDP-ME

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

CDM.1: 24 residues within 4Å: Chain A: P.13, A.14, A.15, G.16, K.27, G.80, S.81, N.82, R.83, T.86, D.107, A.108, A.109, R.110, V.163, T.165, T.191, D.192, K.215 Chain B: S.139, D.140, T.141, R.157 Ligands: MG.2 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.165, A:D.192 Hydrogen bonds: A:A.14, A:A.15, A:G.16, A:G.80, A:T.86, A:A.108, A:A.109, A:R.110, A:V.163, B:T.141, B:R.157 Water bridges: A:K.27, A:K.27, A:A.28, B:R.157, B:R.157, B:R.157, B:R.157 Salt bridges: A:K.27, A:K.215, A:K.215, B:R.157 CDM.5: 24 residues within 4Å: Chain A: D.140, T.141, R.157 Chain B: P.13, A.14, A.15, G.16, K.27, G.80, S.81, N.82, R.83, T.86, D.107, A.108, A.109, R.110, V.163, T.165, T.191, D.192, K.215 Ligands: MG.6, CL.7 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.165, B:D.192 Hydrogen bonds: B:A.14, B:A.15, B:G.16, B:G.80, B:T.86, B:A.108, B:A.109, B:R.110, B:V.163, A:T.141, A:R.157 Water bridges: B:K.27, B:K.27, B:K.215, B:K.215 Salt bridges: B:K.27, B:K.215, B:K.215, A:R.157

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

MG.2: 2 residues within 4Å: Ligands: CDM.1, CL.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: CDM.5 No protein-ligand interaction detected (PLIP)

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

CL.3: 5 residues within 4Å: Chain A: G.16, S.17, G.18, K.27 Ligands: CL.4 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: S.17, G.18, E.19, R.20 Ligands: MG.2, CL.3 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: G.16, S.17, G.18, K.27 Ligands: CDM.5 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: G.18, E.19, R.20, L.21, K.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddy, M.C.M. et al., Crystal Structure of Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): a candidate antitubercular drug target. Proteins (2011)

Release Date

2011-05-04

Peptides

2-C-methyl-D-erythritol 4-phosphate cytidyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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