SMTL ID : 4j6w.1

Crystal structure of HFQ from Pseudomonas aeruginosa in complex with CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 9 residues within 4Å: Chain A: Y.25, G.29, K.31, S.60, T.61 Chain E: L.26, N.28, I.30, L.32 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.29, A:S.60, A:S.60, E:N.28 Water bridges: A:Y.25, A:G.29 Salt bridges: A:K.31, A:K.31 pi-Stacking: A:Y.25 CTP.5: 18 residues within 4Å: Chain A: F.42, Y.55, H.57 Chain B: H.5, Q.8, Q.41, F.42, K.56, H.57 Ligands: C5P.2, MG.6, MG.9, MG.10, C5P.11, MG.15, C5P.16, MG.20, CDP.21 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.42 Hydrogen bonds: B:H.5, B:Q.8, B:K.56 Water bridges: B:H.57, B:H.57, A:H.57, A:H.57 Salt bridges: B:H.57, B:H.57 pi-Stacking: A:F.42 CTP.7: 8 residues within 4Å: Chain C: Y.25, G.29, K.31, S.60, T.61 Chain F: L.26, N.28, I.30 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.29, C:S.60, C:S.60, F:N.28 Water bridges: C:G.29 Salt bridges: C:K.31, C:K.31 pi-Stacking: C:Y.25 CTP.12: 8 residues within 4Å: Chain B: L.26, N.28, I.30 Chain D: Y.25, G.29, K.31, S.60, T.61 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.25 Hydrogen bonds: D:Y.25, D:G.29, D:S.60, D:S.60, B:N.28 Water bridges: D:Y.25 Salt bridges: D:K.31, D:K.31 CTP.17: 8 residues within 4Å: Chain C: L.26, N.28, I.30 Chain E: Y.25, G.29, K.31, S.60, T.61 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.29, E:S.60, E:S.60, C:N.28 Water bridges: E:K.31, E:K.31 Salt bridges: E:K.31, E:K.31 pi-Stacking: E:Y.25 CTP.22: 8 residues within 4Å: Chain D: L.26, N.28, I.30 Chain F: Y.25, G.29, K.31, S.60, T.61 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.29, F:S.60, F:S.60, F:T.61, D:N.28 Water bridges: F:Y.25, F:K.31, F:K.31 Salt bridges: F:K.31 pi-Stacking: F:Y.25

4 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 13 residues within 4Å: Chain A: H.5, Q.8, Q.41, F.42, K.56, H.57 Chain E: F.42, Y.55, H.57 Ligands: CTP.5, C5P.16, MG.19, MG.20 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Q.41, A:F.42 Hydrogen bonds: A:Q.8, A:Q.41, E:H.57 Water bridges: A:H.57 C5P.8: 14 residues within 4Å: Chain C: H.5, Q.8, Q.41, F.42, K.56 Chain F: F.42, Y.55, H.57 Ligands: MG.9, MG.10, C5P.16, MG.19, CDP.21, NA.25 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:Q.41 Hydrogen bonds: C:H.5, C:Q.8, C:K.56, C:K.56 Water bridges: C:H.5, C:H.57 pi-Stacking: F:F.42 C5P.11: 16 residues within 4Å: Chain B: F.42, Y.55, H.57 Chain D: H.5, Q.8, Q.41, F.42, K.56, H.57 Ligands: CTP.5, MG.6, MG.10, MG.14, MG.15, CDP.21, NA.25 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Q.41, D:F.42 Hydrogen bonds: D:H.5, D:Q.8, D:K.56, B:H.57 C5P.16: 15 residues within 4Å: Chain C: F.42, Y.55, H.57 Chain E: G.4, Q.8, Q.41, F.42, K.56, H.57 Ligands: C5P.2, CTP.5, C5P.8, MG.9, MG.19, MG.20 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:F.42 Hydrogen bonds: E:G.4, E:G.4, E:Q.8, E:K.56, C:H.57 Water bridges: E:H.57, C:H.57 Salt bridges: E:H.57 pi-Stacking: C:F.42

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

MG.3: 4 residues within 4Å: Chain A: D.9, F.39, D.40, K.56 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.40 MG.6: 2 residues within 4Å: Ligands: CTP.5, C5P.11 4 PLIP interactions: 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.4, H2O.4, H2O.8, C5P.11 MG.9: 6 residues within 4Å: Chain C: H.57 Ligands: CTP.5, C5P.8, MG.10, C5P.16, CDP.21 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: C5P.8 MG.10: 6 residues within 4Å: Ligands: CTP.5, C5P.8, MG.9, C5P.11, CDP.21, NA.25 3 PLIP interactions: 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.3, H2O.4, C5P.8 MG.14: 6 residues within 4Å: Chain D: F.42, Y.55, K.56, H.57 Ligands: C5P.11, CDP.21 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:F.42 MG.15: 3 residues within 4Å: Ligands: CTP.5, C5P.11, CDP.21 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.4, C5P.11 MG.19: 4 residues within 4Å: Chain E: F.42 Ligands: C5P.2, C5P.8, C5P.16 4 PLIP interactions: 2 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.3, C5P.16, C5P.16 MG.20: 5 residues within 4Å: Chain A: H.57 Chain E: H.57 Ligands: C5P.2, CTP.5, C5P.16 3 PLIP interactions: 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.10, C5P.16

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

NA.4: 1 residues within 4Å: Ligands: P6G.13 No protein-ligand interaction detected (PLIP) NA.24: 5 residues within 4Å: Chain F: T.14, E.18, R.66, V.68, R.69 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.66, F:R.69 NA.25: 4 residues within 4Å: Ligands: C5P.8, MG.10, C5P.11, CDP.21 No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.13: 8 residues within 4Å: Chain A: V.27, N.28 Chain B: V.27 Chain C: V.27 Chain D: V.27 Chain E: V.27 Chain F: V.27 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.27

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 2 residues within 4Å: Chain E: I.30, K.31 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain D: S.51 Chain F: P.67, V.68, L.70 Ligand excluded by PLIP

1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.21: 18 residues within 4Å: Chain C: H.57 Chain D: F.42, Y.55, H.57 Chain F: G.4, Q.8, Q.41, F.42, K.56, H.57 Ligands: CTP.5, C5P.8, MG.9, MG.10, C5P.11, MG.14, MG.15, NA.25 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:F.42 Hydrogen bonds: F:G.4, F:G.4, F:Q.8, F:K.56, D:H.57 Water bridges: F:H.57, F:H.57, D:H.57 Salt bridges: F:H.57, F:H.57 pi-Stacking: D:F.42

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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