SMTL ID : 5ded.1 (1 other biounit)

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-tetramer

Ligands

6 x 0O2: guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)(Non-covalent)

0O2.1: 17 residues within 4Å: Chain A: R.53, K.55, K.63, R.66, D.79, R.112, Y.114, K.119, S.121, Y.123, H.127, E.146, Q.148, W.157, A.158, E.161, H.162 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Y.114, A:S.121, A:Q.148, A:A.158, A:H.162, A:H.162 Salt bridges: A:R.53, A:K.55, A:K.55, A:K.63, A:K.63, A:R.66, A:R.112, A:R.112, A:K.119, A:K.119, A:H.127, A:E.161, A:H.162, A:H.162 pi-Stacking: A:Y.123, A:Y.123 0O2.2: 14 residues within 4Å: Chain A: K.28, K.32, E.48, F.49, V.50, T.51 Chain B: K.28, K.32, R.35, F.49, T.51, M.86, N.155 Ligands: MG.4 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Salt bridges: A:K.28, A:K.32, A:K.32, A:K.32, A:K.32, A:E.48, B:K.28, B:K.32, B:K.32, B:K.32, B:R.35, B:R.35 pi-Stacking: A:F.49, A:F.49 Hydrogen bonds: B:N.155 0O2.3: 19 residues within 4Å: Chain B: R.53, K.55, K.63, R.66, K.67, D.79, R.84, R.112, Y.114, K.119, S.121, Y.123, H.127, E.146, Q.148, W.157, A.158, E.161, H.162 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:R.53, B:D.79, B:R.84, B:Y.114, B:K.119, B:S.121, B:A.158, B:H.162 Salt bridges: B:R.53, B:K.55, B:K.55, B:K.63, B:K.63, B:K.63, B:K.63, B:R.66, B:K.67, B:K.67, B:R.112, B:R.112, B:K.119, B:K.119, B:H.127, B:E.161, B:H.162 pi-Stacking: B:Y.123, B:Y.123 0O2.5: 17 residues within 4Å: Chain C: K.55, K.63, R.66, D.79, R.84, R.112, Y.114, K.119, S.121, Y.123, H.127, E.146, Q.148, W.157, A.158, E.161, H.162 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:R.84, C:K.119, C:S.121, C:Q.148, C:A.158, C:H.162 Salt bridges: C:K.55, C:K.55, C:K.63, C:K.63, C:R.66, C:R.112, C:R.112, C:K.119, C:K.119, C:K.119, C:H.127, C:E.161, C:H.162 pi-Stacking: C:Y.123, C:Y.123 0O2.6: 17 residues within 4Å: Chain D: R.53, K.55, K.63, R.66, K.67, D.79, R.112, Y.114, K.119, S.121, Y.123, H.127, E.146, Q.148, A.158, E.161, H.162 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:R.53, D:R.66, D:K.119, D:S.121, D:Q.148, D:A.158, D:H.162 Salt bridges: D:R.53, D:K.55, D:K.55, D:K.63, D:K.63, D:K.63, D:K.67, D:R.112, D:K.119, D:K.119, D:H.127, D:E.161, D:H.162, D:H.162 pi-Stacking: D:Y.123, D:Y.123 0O2.7: 13 residues within 4Å: Chain C: K.28, K.32, R.35, F.49, T.51, T.159 Chain D: K.32, R.35, E.48, F.49, V.50, T.51 Ligands: MG.8 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:R.35, D:E.48 Salt bridges: D:K.32, D:K.32, D:E.48, C:K.28, C:K.32, C:K.32, C:K.32, C:K.32, C:R.35, C:R.35 pi-Stacking: D:F.49

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: K.32 Ligands: 0O2.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: K.28 Ligands: 0O2.7 No protein-ligand interaction detected (PLIP)

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

2015-10-28

Peptides

GTP pyrophosphokinase YjbM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
F

D
G

GTP pyrophosphokinase YjbM

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