SMTL ID : 4mml.1

D40A Hfq from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: A.40, Q.41, F.42, V.43 Chain E: S.6, L.7, Q.8 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:S.6, E:L.7, E:Q.8, E:Q.8, A:Q.41, A:F.42, A:V.43 SO4.4: 7 residues within 4Å: Chain B: A.40, Q.41, F.42, V.43 Chain F: S.6, L.7, Q.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:Q.41, B:F.42, B:V.43, F:S.6, F:L.7, F:Q.8, F:Q.8 SO4.7: 7 residues within 4Å: Chain C: A.40, Q.41, F.42, V.43 Chain D: S.6, L.7, Q.8 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.6, D:L.7, D:Q.8, D:Q.8, C:Q.41, C:F.42, C:V.43 SO4.10: 7 residues within 4Å: Chain B: S.6, L.7, Q.8 Chain D: A.40, Q.41, F.42, V.43 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:S.6, B:L.7, B:Q.8, B:Q.8, D:Q.41, D:F.42, D:V.43 SO4.13: 7 residues within 4Å: Chain C: S.6, L.7, Q.8 Chain E: A.40, Q.41, F.42, V.43 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:S.6, C:L.7, C:Q.8, C:Q.8, E:Q.41, E:F.42, E:V.43 SO4.16: 7 residues within 4Å: Chain A: S.6, L.7, Q.8 Chain F: A.40, Q.41, F.42, V.43 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:Q.41, F:F.42, F:V.43, A:S.6, A:L.7, A:Q.8, A:Q.8

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

MG.2: 5 residues within 4Å: Ligands: MG.5, MG.8, MG.11, MG.14, MG.17 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Ligands: MG.2, MG.8, MG.11, MG.14, MG.17 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Ligands: MG.2, MG.5, MG.11, MG.14, MG.17 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Ligands: MG.2, MG.5, MG.8, MG.14, MG.17 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Ligands: MG.2, MG.5, MG.8, MG.11, MG.17 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Ligands: MG.2, MG.5, MG.8, MG.11, MG.14 No protein-ligand interaction detected (PLIP)

6 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.3: 10 residues within 4Å: Chain A: Q.8, Q.41, F.42, K.56, H.57 Chain F: F.42, Y.55, H.57 Ligands: U5P.15, U5P.18 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:Q.41, A:F.42 Hydrogen bonds: A:Q.8, A:Q.41 Water bridges: A:K.56, F:H.57 pi-Stacking: F:F.42 U5P.6: 10 residues within 4Å: Chain B: Q.8, Q.41, F.42, K.56, H.57 Chain D: F.42, Y.55, H.57 Ligands: U5P.12, U5P.18 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Water bridges: D:H.57, B:K.56 pi-Stacking: D:F.42 Hydrophobic interactions: B:Q.41, B:F.42 Hydrogen bonds: B:Q.8, B:Q.41 U5P.9: 10 residues within 4Å: Chain C: Q.8, Q.41, F.42, K.56, H.57 Chain E: F.42, Y.55, H.57 Ligands: U5P.12, U5P.15 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:Q.41, C:F.42 Hydrogen bonds: C:Q.8, C:Q.41 Water bridges: C:K.56, E:H.57 pi-Stacking: E:F.42 U5P.12: 10 residues within 4Å: Chain C: F.42, Y.55, H.57 Chain D: Q.8, Q.41, F.42, K.56, H.57 Ligands: U5P.6, U5P.9 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.41, D:F.42 Hydrogen bonds: D:Q.8, D:Q.41 Water bridges: D:K.56, C:H.57 pi-Stacking: C:F.42 U5P.15: 10 residues within 4Å: Chain A: F.42, Y.55, H.57 Chain E: Q.8, Q.41, F.42, K.56, H.57 Ligands: U5P.3, U5P.9 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Q.41, E:F.42 Hydrogen bonds: E:Q.8, E:Q.41 Water bridges: E:K.56, A:H.57 pi-Stacking: A:F.42 U5P.18: 10 residues within 4Å: Chain B: F.42, Y.55, H.57 Chain F: Q.8, Q.41, F.42, K.56, H.57 Ligands: U5P.3, U5P.6 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain F Water bridges: B:H.57, F:K.56 pi-Stacking: B:F.42 Hydrophobic interactions: F:Q.41, F:F.42 Hydrogen bonds: F:Q.8, F:Q.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murina, V.N. et al., Effect of conserved intersubunit amino Acid substitutions on hfq protein structure and stability. Biochemistry Mosc. (2014)

Release Date

2014-07-09

Peptides

Protein hfq: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Protein hfq