SMTL ID : 4x9c.1

1.4A crystal structure of Hfq from Methanococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

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

PEG.1: 8 residues within 4Å: Chain A: Y.48, E.49, F.62, H.64 Chain B: E.18, A.20, N.47, K.63 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.63, A:E.49, A:H.64 Water bridges: B:K.63 PEG.5: 6 residues within 4Å: Chain B: K.27, V.28, K.29, D.39, E.70, Y.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.39 Water bridges: B:V.28, B:E.70, B:Y.71 PEG.11: 8 residues within 4Å: Chain C: Y.48, F.62, H.64 Chain D: N.47, Y.48, K.63, H.64 Ligands: NA.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.63, D:K.63, D:H.64, C:H.64 Water bridges: D:H.64 PEG.13: 8 residues within 4Å: Chain D: Y.48, F.62, H.64 Chain E: N.47, Y.48, K.63, H.64 Ligands: SO4.18 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.63, D:H.64 Water bridges: E:E.18, E:N.47, E:H.64 PEG.19: 4 residues within 4Å: Chain F: E.36, V.37, L.38, R.57 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:R.57 Water bridges: F:R.57, A:Y.68 PEG.20: 7 residues within 4Å: Chain A: N.47, Y.48, K.63, H.64 Chain F: Y.48, H.64 Ligands: NA.22 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:N.47, F:H.64 Water bridges: A:H.64, A:H.64

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: K.27, K.29, E.70, Y.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27 Water bridges: A:E.70

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: L.32, R.33, G.35, D.67 Chain F: N.34, E.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Water bridges: A:L.32 Hydrogen bonds: F:N.34 EDO.4: 5 residues within 4Å: Chain A: T.43, M.51 Chain B: Y.19, Y.71 Ligands: EDO.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.71, B:Y.71, A:T.43 Water bridges: B:Y.19 EDO.7: 3 residues within 4Å: Chain B: Y.19, R.22 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.22 EDO.9: 1 residues within 4Å: Chain C: R.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.22, C:Y.71 EDO.10: 4 residues within 4Å: Chain C: K.27, V.28, K.29, E.70 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.27, C:K.29, C:E.70 EDO.17: 6 residues within 4Å: Chain E: K.27, D.39, E.41, K.53, V.54, G.55 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.27, E:E.41, E:K.53, E:G.55

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

NA.6: 4 residues within 4Å: Chain B: M.51, V.52, L.59 Chain C: Y.71 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.43, B:V.52, B:L.59, C:Y.71 NA.8: 3 residues within 4Å: Chain C: H.64 Chain D: H.64 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.64 NA.15: 5 residues within 4Å: Chain D: R.33, N.34 Chain E: R.33, D.67 Ligands: CL.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.33 NA.16: 4 residues within 4Å: Chain E: M.51, V.52, L.59 Chain F: Y.71 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.43, E:V.52, E:L.59, F:Y.71 NA.22: 6 residues within 4Å: Chain A: E.18, A.20, K.63 Chain F: E.49, F.62 Ligands: PEG.20 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:E.49, A:K.63

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

CL.12: 3 residues within 4Å: Chain D: R.33 Chain E: R.33 Ligands: NA.15 Ligand excluded by PLIP

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.14: 4 residues within 4Å: Chain E: N.24, G.25, K.26, Y.71 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.26 Water bridges: E:N.24 PG4.21: 4 residues within 4Å: Chain F: N.24, G.25, K.26, Y.71 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.26 Water bridges: F:R.22, F:N.24

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

SO4.18: 6 residues within 4Å: Chain E: Y.48, F.62, H.64 Chain F: Y.48, K.63 Ligands: PEG.13 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain E Water bridges: F:N.47, F:K.63, F:K.63, F:K.63, E:H.64, E:H.64, E:H.64 Salt bridges: E:H.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikulin, A. et al., Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii. J. Biomol. Struct. Dyn. (2017)

Release Date

2014-12-24

Peptides

Uncharacterized protein MJ1435: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uncharacterized protein MJ1435

Related Entries With Identical Sequence