SMTL ID : 6ex0.1

Crystal structure of RelP (SAS2) from Staphylococcus aureus bound to pppGpp in the post-catalytic state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-tetramer

Ligands

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

0O2.1: 15 residues within 4Å: Chain A: R.78, K.88, D.107, R.112, K.147, N.149, Y.151, H.155, E.174, Q.176, A.186, S.187, E.189, H.190, R.193 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.78, A:R.91, A:R.112, A:N.149, A:Q.176, A:A.186, A:H.190, A:R.193 Salt bridges: A:K.88, A:K.88, A:R.112, A:K.138, A:K.147, A:E.189, A:H.190, A:H.190, A:R.193 pi-Stacking: A:Y.151, A:Y.151 pi-Cation interactions: A:R.193 0O2.2: 16 residues within 4Å: Chain B: R.78, K.80, K.88, R.91, K.92, D.107, R.112, K.147, N.149, Y.151, H.155, Q.176, A.186, E.189, H.190, R.193 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:D.107, B:R.112, B:N.149, B:Q.176, B:A.186 Salt bridges: B:R.78, B:K.80, B:K.88, B:K.88, B:R.91, B:R.91, B:K.92, B:R.112, B:K.147, B:E.189, B:H.190, B:H.190, B:R.193 pi-Stacking: B:Y.151, B:Y.151 pi-Cation interactions: B:R.193 0O2.4: 15 residues within 4Å: Chain C: R.78, K.88, D.107, R.112, K.147, N.149, Y.151, H.155, E.174, Q.176, A.186, S.187, E.189, H.190, R.193 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:R.78, C:R.91, C:R.112, C:N.149, C:Q.176, C:A.186, C:H.190, C:H.190, C:R.193 Salt bridges: C:K.88, C:K.88, C:R.112, C:K.138, C:K.147, C:E.189, C:H.190, C:H.190, C:R.193 pi-Stacking: C:Y.151, C:Y.151 pi-Cation interactions: C:R.193 0O2.5: 16 residues within 4Å: Chain D: R.78, K.80, K.88, R.91, K.92, D.107, R.112, K.147, N.149, Y.151, H.155, Q.176, A.186, E.189, H.190, R.193 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:D.107, D:R.112, D:N.149, D:Q.176, D:A.186, D:H.190 Salt bridges: D:R.78, D:K.80, D:K.88, D:K.88, D:R.91, D:R.91, D:K.92, D:R.112, D:K.147, D:E.189, D:H.190, D:H.190, D:R.193 pi-Stacking: D:Y.151, D:Y.151 pi-Cation interactions: D:R.193

2 x FE2: FE (II) ION(Non-covalent)

FE2.3: 2 residues within 4Å: Chain A: E.51 Chain B: E.51 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.51, H2O.1, H2O.1, H2O.1, H2O.1 FE2.6: 2 residues within 4Å: Chain C: E.51 Chain D: E.51 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.51, H2O.2, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manav, M.C. et al., Structural basis for (p)ppGpp synthesis by theStaphylococcus aureussmall alarmone synthetase RelP. J. Biol. Chem. (2018)

Release Date

2018-01-24

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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