SMTL ID : 1i52.1

CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: L.46 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:L.46, H2O.1, H2O.5, H2O.5, H2O.5 CA.4: 1 residues within 4Å: Chain B: L.46 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:L.46, H2O.13, H2O.18, H2O.18, H2O.18

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

MG.2: 1 residues within 4Å: Ligands: CTP.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: CTP.6 No protein-ligand interaction detected (PLIP)

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

CTP.3: 19 residues within 4Å: Chain A: P.13, A.14, A.15, G.16, F.17, G.18, R.19, R.20, K.27, Q.28, G.82, D.83, E.84, R.85, S.88, D.106, A.107, A.108 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:A.15, A:G.16, A:F.17, A:G.18, A:R.19, A:R.20, A:G.82, A:S.88, A:A.107, A:A.108 Water bridges: A:R.19, A:R.20, A:R.20, A:R.20, A:K.27, A:Q.28, A:Q.28, A:K.213, A:K.213 Salt bridges: A:R.19, A:R.20, A:R.20, A:K.27, A:K.27, A:K.27, A:K.213 CTP.6: 19 residues within 4Å: Chain B: P.13, A.14, A.15, G.16, F.17, G.18, R.19, R.20, K.27, Q.28, G.82, D.83, E.84, R.85, S.88, D.106, A.107, A.108 Ligands: MG.5 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:A.15, B:G.16, B:F.17, B:G.18, B:R.19, B:R.20, B:G.82, B:S.88, B:A.107, B:A.108 Water bridges: B:R.19, B:R.20, B:R.20, B:R.20, B:K.27, B:Q.28, B:Q.28, B:K.213, B:K.213 Salt bridges: B:R.19, B:R.20, B:R.20, B:K.27, B:K.27, B:K.27, B:K.213

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

2001-07-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE

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