SMTL ID : 6ott.1

Structure of PurF in complex with ppApp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: R.45 Chain C: R.45 Ligands: N7Y.2, MG.5, N7Y.6 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain B: R.45 Chain D: R.45 Ligands: N7Y.4, MG.7, N7Y.8 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: R.45 Chain C: R.45 Ligands: MG.1, N7Y.2, N7Y.6 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: R.45 Chain D: R.45 Ligands: MG.3, N7Y.4, N7Y.8 No protein-ligand interaction detected (PLIP)

4 x N7Y: adenosine 3',5'-bis(trihydrogen diphosphate)(Non-covalent)

N7Y.2: 20 residues within 4Å: Chain A: R.43, R.45, K.46, R.58, H.59, R.62 Chain C: R.45, K.46, A.47, N.48, H.59, R.62, S.81, A.82, S.83, E.84, Q.492 Ligands: MG.1, MG.5, N7Y.6 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:R.45, C:A.82, A:H.59, A:R.62 Salt bridges: C:R.45, C:R.45, C:H.59, C:R.62, A:R.45, A:R.45, A:R.58, A:H.59 pi-Cation interactions: A:R.62 N7Y.4: 19 residues within 4Å: Chain B: R.45, K.46, R.58, H.59, R.62 Chain D: R.45, K.46, A.47, N.48, H.59, R.62, S.81, A.82, S.83, E.84, Q.492 Ligands: MG.3, MG.7, N7Y.8 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:R.45, D:A.82, B:H.59, B:R.62 Salt bridges: D:R.45, D:R.45, D:H.59, D:R.62, B:R.45, B:R.45, B:R.58, B:H.59 pi-Cation interactions: B:R.62 N7Y.6: 20 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.43, R.45, K.46, R.58, H.59, R.62 Ligands: MG.1, N7Y.2, MG.5 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:H.59, C:R.62, A:R.45, A:A.82 Salt bridges: C:R.45, C:R.45, C:R.58, C:H.59, A:R.45, A:R.45, A:H.59, A:R.62 pi-Cation interactions: C:R.62 N7Y.8: 19 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, K.46, R.58, H.59, R.62 Ligands: MG.3, N7Y.4, MG.7 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:H.59, D:R.62, B:R.45, B:A.82 Salt bridges: D:R.45, D:R.45, D:R.58, D:H.59, B:R.45, B:R.45, B:H.59, B:R.62 pi-Cation interactions: D:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, S. et al., An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp. Nature (2019)

Release Date

2019-11-06

Peptides

Amidophosphoribosyltransferase, PurF: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Amidophosphoribosyltransferase, PurF

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