SMTL ID : 4j5y.1

Crystal structure of Hfq from Pseudomonas aeruginosa in complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 9 residues within 4Å: Chain A: Y.25, K.31, T.61, V.63 Chain F: L.26, I.30, L.32, Q.52 Ligands: NA.2 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:Q.52, F:Q.52, A:Y.25, A:Y.25 Salt bridges: A:K.31 pi-Stacking: A:Y.25, A:Y.25 ATP.3: 9 residues within 4Å: Chain A: L.26, I.30, Q.52 Chain B: Y.25, G.29, K.31, S.60, T.61, V.63 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.25, B:G.29, B:T.61, A:Q.52, A:Q.52 Water bridges: B:S.60 Salt bridges: B:K.31, B:K.31 pi-Stacking: B:Y.25, B:Y.25 ATP.4: 9 residues within 4Å: Chain B: L.26, I.30, L.32, Q.52 Chain C: Y.25, G.29, K.31, T.61, V.63 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.25, C:T.61, B:Q.52, B:Q.52 Salt bridges: C:K.31 pi-Stacking: C:Y.25, C:Y.25 ATP.5: 9 residues within 4Å: Chain C: L.26, I.30, L.32, Q.52 Chain D: Y.25, K.31, T.61, V.63 Ligands: NA.7 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.25, D:Y.25, D:T.61, C:Q.52, C:Q.52 Water bridges: D:K.31 Salt bridges: D:K.31 pi-Stacking: D:Y.25, D:Y.25 ATP.8: 9 residues within 4Å: Chain E: L.26, I.30, L.32, Q.52 Chain F: Y.25, G.29, S.60, T.61, V.63 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:Q.52, E:Q.52, F:Y.25, F:Y.25, F:G.29 Water bridges: E:N.28 Salt bridges: F:K.31 pi-Stacking: F:Y.25, F:Y.25

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: G.29 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.29 Water bridges: F:N.28 NA.7: 2 residues within 4Å: Chain D: G.29 Ligands: ATP.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.29 Water bridges: C:N.28

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain D: N.13, R.16, S.38, F.39 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.13, D:F.39 Water bridges: D:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murina, V. et al., Hfq binds ribonucleotides in three different RNA-binding sites. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-07-31

Peptides

Protein hfq: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Protein hfq

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