SMTL ID : 2y6p.1 (1 other biounit)

Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CTP.1: 17 residues within 4Å: Chain A: P.8, A.9, R.10, S.13, T.14, R.15, K.19, L.70, P.71, S.72, G.73, R.76, G.94, D.95, D.219 Ligands: MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:T.14, A:R.15, A:L.70, A:R.76, A:G.94, A:D.95 Water bridges: A:R.15, A:R.15, A:R.15, A:R.15, A:L.16, A:D.219 Salt bridges: A:R.10, A:R.10, A:R.15, A:R.15, A:K.19, A:K.19, A:K.19 CTP.6: 18 residues within 4Å: Chain B: P.8, A.9, R.10, S.13, T.14, R.15, K.19, L.70, P.71, S.72, G.73, R.76, Q.93, G.94, D.95, D.219 Ligands: MG.7, MG.8 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:R.10, B:R.10, B:T.14, B:T.14, B:R.15, B:L.70, B:R.76, B:Q.93, B:G.94, B:D.95 Water bridges: B:R.10, B:R.10, B:R.15, B:R.15, B:R.15, B:R.15, B:L.16, B:G.73, B:N.91 Salt bridges: B:R.10, B:R.10, B:R.15, B:R.15, B:K.19, B:K.19, B:K.19

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.19, D.95, D.219 Ligands: CTP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.95, A:D.219, H2O.1, H2O.1, H2O.3 MG.3: 2 residues within 4Å: Chain A: R.15 Ligands: CTP.1 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: K.19, D.95, D.219 Ligands: CTP.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.95, B:D.219, H2O.4, H2O.6, H2O.7 MG.8: 2 residues within 4Å: Chain B: R.15 Ligands: CTP.6 No protein-ligand interaction detected (PLIP)

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 6 residues within 4Å: Chain A: S.74, Y.170, F.172, F.180, E.195, Q.196 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.172, A:F.180 Hydrogen bonds: A:E.195

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 2 residues within 4Å: Chain A: E.126, E.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, H. et al., Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, an Enzyme Involved in Lipopolysaccharide Biosynthesis. Plos One (2011)

Release Date

2011-08-24

Peptides

3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE

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