SMTL ID : 6czf.1

The structure of E. coli PurF in complex with ppGpp-Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.45 Chain C: R.45 Ligands: G4P.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: R.45 Chain D: R.45 Ligands: G4P.4 No protein-ligand interaction detected (PLIP)

2 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.2: 16 residues within 4Å: Chain A: R.45, K.46, A.47, N.48, H.59, R.62, S.81, A.82, S.83, E.84, Q.492 Chain C: R.45, R.58, H.59, R.62 Ligands: MG.1 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:R.45, A:N.48, A:N.48, A:A.82, A:E.84, A:Q.492, C:R.45, C:R.62 Salt bridges: A:R.45, A:R.45, A:H.59, A:R.62, C:R.45, C:R.58, C:H.59 pi-Cation interactions: C:R.62 G4P.4: 16 residues within 4Å: Chain B: R.45, K.46, A.47, N.48, H.59, R.62, S.81, A.82, S.83, E.84, Q.492 Chain D: R.45, R.58, H.59, R.62 Ligands: MG.3 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:R.45, B:N.48, B:A.82, B:Q.492, D:R.45, D:R.62 Water bridges: B:N.48, B:N.48, B:R.62, B:R.62 Salt bridges: B:R.45, B:R.45, B:H.59, B:R.62, D:R.45, D:R.58, D:H.59 pi-Cation interactions: D:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Affinity-based capture and identification of protein effectors of the growth regulator ppGpp. Nat. Chem. Biol. (2019)

Release Date

2018-10-10

Peptides

Amidophosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Amidophosphoribosyltransferase