SMTL ID : 6fgx.1

Crystal structure of the small alarmone synthethase 2 from Staphylococcus aureus bound to AMPCPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.95, D.114, E.181 Ligands: APC.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, H2O.1 MG.3: 3 residues within 4Å: Chain B: D.114, E.181 Ligands: APC.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.114 MG.5: 4 residues within 4Å: Chain C: K.95, D.114, E.181 Ligands: APC.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.114, H2O.2 MG.7: 3 residues within 4Å: Chain D: D.114, E.181 Ligands: APC.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.114

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

APC.2: 13 residues within 4Å: Chain A: E.83, R.85, K.87, S.91, K.95, R.98, D.114, G.117, I.118, R.119, E.181, Q.183 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.85, A:S.91, A:S.91, A:R.119, A:R.119, A:E.181, A:E.181, A:Q.183 Salt bridges: A:K.87, A:K.95, A:R.98 pi-Cation interactions: A:R.85, A:R.119 APC.4: 13 residues within 4Å: Chain B: E.83, R.85, K.87, S.91, K.95, D.114, G.117, I.118, R.119, E.181, Q.183, H.197 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.85, B:S.91, B:S.91, B:R.119, B:R.119, B:E.181, B:E.181, B:Q.183 Salt bridges: B:K.87, B:K.95 pi-Cation interactions: B:R.85, B:R.119, B:R.119 APC.6: 13 residues within 4Å: Chain C: E.83, R.85, K.87, S.91, K.95, R.98, D.114, G.117, I.118, R.119, E.181, Q.183 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.85, C:S.91, C:S.91, C:R.119, C:R.119, C:E.181, C:Q.183 Salt bridges: C:K.87, C:K.95, C:R.98 pi-Cation interactions: C:R.85, C:R.119 APC.8: 13 residues within 4Å: Chain D: E.83, R.85, K.87, S.91, K.95, D.114, G.117, I.118, R.119, E.181, Q.183, H.197 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:R.85, D:S.91, D:S.91, D:R.119, D:R.119, D:E.181, D:Q.183 Salt bridges: D:K.87, D:K.95 pi-Cation interactions: D:R.85, D:R.119, D:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinchen, W. et al., Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ. Sci Rep (2018)

Release Date

2018-02-07

Peptides

GTP pyrophosphokinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

GTP pyrophosphokinase

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