SMTL ID : 4x9d.1

High-resolution structure of Hfq from Methanococcus jannaschii in complex with UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

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

PGE.1: 5 residues within 4Å: Chain A: K.27, V.28, K.29, E.70, Y.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.70 PGE.15: 3 residues within 4Å: Chain E: N.24, G.25, K.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.24, E:K.26

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

SO4.2: 6 residues within 4Å: Chain A: Y.19, R.22, L.23, K.26, Y.71 Ligands: SO4.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.71 Salt bridges: A:R.22, A:K.26 SO4.19: 7 residues within 4Å: Chain A: Y.19, R.22, Y.71 Chain F: T.43, G.44, M.51 Ligands: SO4.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:R.22, A:Y.71, F:T.43

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

NA.3: 6 residues within 4Å: Chain A: Y.48, F.62, K.63, H.64 Ligands: U5P.4, U5P.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.63, A:H.64, A:H.64 NA.6: 2 residues within 4Å: Chain B: H.64 Ligands: U5P.12 No protein-ligand interaction detected (PLIP) NA.7: 6 residues within 4Å: Chain B: Y.48, F.62, K.63, H.64 Ligands: U5P.8, U5P.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.48, B:K.63, B:H.64 NA.10: 6 residues within 4Å: Chain C: Y.48, F.62, K.63, H.64 Ligands: U5P.12, U5P.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.63, C:H.64, C:H.64 NA.20: 6 residues within 4Å: Chain F: Y.48, F.62, K.63, H.64 Ligands: U5P.4, U5P.21 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.63, F:H.64, F:H.64

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

U5P.4: 11 residues within 4Å: Chain A: E.18, N.47, Y.48, K.63 Chain F: Y.48, F.62, H.64 Ligands: NA.3, U5P.8, NA.20, U5P.21 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.18, A:Y.48, A:Y.48, A:K.63 pi-Stacking: A:Y.48, F:Y.48 U5P.8: 11 residues within 4Å: Chain A: Y.48, F.62, H.64 Chain B: N.47, Y.48, K.63 Ligands: NA.3, U5P.4, NA.7, U5P.12, U5P.21 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.48 Hydrogen bonds: B:K.63 Water bridges: B:E.18, B:N.47 pi-Stacking: A:Y.48 U5P.12: 13 residues within 4Å: Chain B: Y.48, F.62, H.64 Chain C: E.18, N.47, Y.48, K.63, H.64 Ligands: NA.6, NA.7, U5P.8, NA.10, U5P.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C pi-Stacking: B:Y.48, C:Y.48 Hydrogen bonds: C:E.18, C:K.63 Salt bridges: C:H.64 U5P.13: 11 residues within 4Å: Chain C: Y.48, F.62, H.64 Chain D: E.18, N.47, Y.48, K.63, H.64 Ligands: NA.10, U5P.12, U5P.17 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D pi-Stacking: C:Y.48 Hydrophobic interactions: D:Y.48 Hydrogen bonds: D:E.18, D:K.63 Water bridges: D:K.63, D:H.64 Salt bridges: D:H.64 U5P.17: 11 residues within 4Å: Chain D: Y.48, F.62, H.64 Chain E: E.18, N.47, Y.48, F.62, K.63, H.64 Ligands: U5P.13, U5P.21 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:N.47 Hydrogen bonds: E:E.18, E:E.18, E:Y.48, E:K.63, E:K.63, E:H.64 Water bridges: E:N.16 Salt bridges: E:H.64 pi-Stacking: E:Y.48, D:Y.48 U5P.21: 12 residues within 4Å: Chain E: Y.48, F.62, H.64 Chain F: E.18, N.47, Y.48, K.63, H.64 Ligands: U5P.4, U5P.8, U5P.17, NA.20 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.18, F:E.18, F:K.63 pi-Stacking: F:Y.48, E:Y.48

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

EDO.5: 4 residues within 4Å: Chain B: K.27, K.29, D.39, Y.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.39, B:Y.71

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

PG4.9: 5 residues within 4Å: Chain B: T.43, M.51 Chain C: R.22, K.26, Y.71 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.22, C:Y.71, B:T.43, B:T.43 Water bridges: C:K.26 PG4.14: 6 residues within 4Å: Chain E: K.27, V.28, K.29, D.39, E.70, Y.71 No protein-ligand interaction detected (PLIP)

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

CL.11: 2 residues within 4Å: Chain C: T.43, M.51 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain E: T.43, M.51 Ligand excluded by PLIP

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

PEG.18: 5 residues within 4Å: Chain A: Y.68 Chain F: E.36, V.37, L.38, R.57 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Y.68, F:R.57

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

2015-12-23

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

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