SMTL ID : 3qui.1

Crystal structure of Pseudomonas aeruginosa Hfq in complex with ADPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-hexamer

Ligands

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

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

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 10 residues within 4Å: Chain C: L.26, I.30, L.32, Q.52 Chain D: Y.25, G.29, K.31, S.60, T.61, V.63 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.29, D:K.31, C:Q.52, C:Q.52 Water bridges: D:K.31, D:S.60 pi-Stacking: D:Y.25, D:Y.25 ANP.5: 7 residues within 4Å: Chain C: F.42, H.57 Chain D: Q.8, Q.41, F.42, H.57 Chain E: H.57 8 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D, 1 interactions with chain E Water bridges: C:H.57, D:H.57 pi-Stacking: C:F.42, C:F.42 Hydrogen bonds: D:Q.8, D:Q.41, E:H.57 Salt bridges: D:H.57 ANP.7: 6 residues within 4Å: Chain D: L.32, Q.52 Chain E: Y.25, K.31, T.61, V.63 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.52, D:Q.52, E:Y.25 pi-Stacking: E:Y.25, E:Y.25

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

PEG.6: 4 residues within 4Å: Chain D: E.18, P.21, S.65, R.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.18, D:R.66

1 x ADE: ADENINE(Non-covalent)

ADE.8: 6 residues within 4Å: Chain E: I.30, L.32, Q.52 Chain F: Y.25, T.61, V.63 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E pi-Stacking: F:Y.25, F:Y.25 Hydrogen bonds: E:Q.52 Water bridges: E:N.28

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

2012-02-08

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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