SMTL ID : 5f2v.3 (2 other biounits)

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to AMPCPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 16 residues within 4Å: Chain A: T.42, G.43, R.44, K.46, P.47, S.50, K.54, R.57, D.70, G.73, L.74, R.75, E.137, Q.139, H.153 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.50, A:R.75, A:R.75, A:E.137, A:E.137, A:Q.139 Salt bridges: A:K.46, A:K.54, A:R.57 pi-Cation interactions: A:R.44, A:R.75 APC.3: 16 residues within 4Å: Chain B: T.42, G.43, R.44, K.46, P.47, S.50, K.54, R.57, D.70, G.73, L.74, R.75, E.137, Q.139, H.153 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.44, B:K.46, B:S.50, B:R.75, B:R.75, B:E.137, B:Q.139 Salt bridges: B:K.46, B:K.54, B:R.57 pi-Cation interactions: B:R.44, B:R.75 APC.5: 16 residues within 4Å: Chain C: T.42, G.43, R.44, K.46, P.47, S.50, K.54, R.57, D.70, G.73, L.74, R.75, E.137, Q.139, H.153 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.44, C:K.46, C:S.50, C:D.70, C:R.75, C:R.75, C:E.137, C:E.137, C:Q.139 Salt bridges: C:K.46, C:K.54, C:R.57 pi-Cation interactions: C:R.44, C:R.75, C:R.75 APC.7: 14 residues within 4Å: Chain D: T.42, G.43, R.44, K.46, S.50, K.54, D.70, G.73, L.74, R.75, E.137, Q.139, H.153 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.46, D:K.46, D:S.50, D:R.75, D:R.75, D:E.137, D:Q.139 Salt bridges: D:K.46, D:K.54 pi-Cation interactions: D:R.44, D:R.75

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.46, D.70, E.137 Ligands: APC.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.70 MG.4: 4 residues within 4Å: Chain B: K.46, D.70, E.137 Ligands: APC.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.70, H2O.1 MG.6: 3 residues within 4Å: Chain C: D.70, E.137 Ligands: APC.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.70, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain D: D.70, E.137 Ligands: APC.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinchen, W. et al., Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-12-16

Peptides

GTP pyrophosphokinase YjbM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
R

D
Q

GTP pyrophosphokinase YjbM

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