SMTL ID : 1ini.1

CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.20 Ligands: CDM.2 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: R.20 Ligands: CDM.4 No protein-ligand interaction detected (PLIP)

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

CDM.2: 25 residues within 4Å: Chain A: P.13, A.14, A.15, G.16, R.20, K.27, G.82, D.83, E.84, R.85, S.88, D.106, A.107, A.108, R.109, A.163, T.165, T.189, D.190, K.213, T.215 Chain B: D.139, T.140, R.157 Ligands: MG.1 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.165, A:D.190 Hydrogen bonds: A:A.15, A:G.16, A:R.20, A:G.82, A:S.88, A:A.107, A:A.108, A:R.109, A:A.163, B:D.139, B:T.140, B:R.157 Salt bridges: A:R.20, A:K.27, A:K.213, A:K.213, B:R.157 CDM.4: 25 residues within 4Å: Chain A: D.139, T.140, R.157 Chain B: P.13, A.14, A.15, G.16, R.20, K.27, G.82, D.83, E.84, R.85, S.88, D.106, A.107, A.108, R.109, A.163, T.165, T.189, D.190, K.213, T.215 Ligands: MG.3 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:T.140, A:T.140, A:R.157, B:A.15, B:G.16, B:R.20, B:G.82, B:S.88, B:A.107, B:A.108, B:R.109, B:A.163 Salt bridges: A:R.157, B:R.20, B:K.27, B:K.213, B:K.213 Hydrophobic interactions: B:T.165, B:D.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richard, S.B. et al., Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. Nat.Struct.Biol. (2001)

Release Date

2001-11-14

Peptides

4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE

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