SMTL ID : 3rer.1

Crystal structure of E. coli Hfq in complex with AU6A RNA and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

1 x A- U- U- U- U- U- U- A: 5'-R(*AP*UP*UP*UP*UP*UP*UP*A)-3'(Non-covalent)

A-U-U-U-U-U-U-A.1: 37 residues within 4Å: Chain A: Q.8, Q.41, F.42, Y.55, K.56, H.57 Chain B: S.6, Q.8, D.9, Q.41, F.42, Y.55, K.56, H.57 Chain C: Q.5, Q.8, Q.41, F.42, K.56, H.57 Chain D: Q.8, Q.41, F.42, Y.55, K.56, H.57 Chain E: Q.41, F.42, Y.55, H.57 Chain F: Q.5, Q.8, Q.41, F.42, K.56, H.57 Ligands: MG.8 Protein-ligand interaction information (PLIP) not available

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

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

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

MG.4: 1 residues within 4Å: Chain B: S.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.6, H2O.3, H2O.5, H2O.16, H2O.16 MG.8: 2 residues within 4Å: Ligands: A-U-U-U-U-U-U-A.1, A-U-U-U-U-U-U-A.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Cooperation of Escherichia coli Hfq hexamers in DsrA binding. Genes Dev. (2011)

Release Date

2011-10-19

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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