SMTL ID : 5szd.2 (2 other biounits)

Crystal structure of Aquifex aeolicus Hfq at 1.5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-hexamer

Ligands

6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 6 residues within 4Å: Chain A: F.43, Y.57, H.59 Chain B: Q.9, L.42, H.59 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.42, A:F.43, A:F.43, A:F.43 Hydrogen bonds: B:Q.9, A:H.59 MRD.6: 6 residues within 4Å: Chain B: F.43, Y.57, H.59 Chain C: Q.9, L.42, H.59 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.42, B:F.43, B:F.43 Hydrogen bonds: C:Q.9, B:H.59 MRD.11: 6 residues within 4Å: Chain C: F.43, Y.57, H.59 Chain D: Q.9, L.42, H.59 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.42, C:F.43, C:F.43, C:F.43 Hydrogen bonds: D:Q.9, C:H.59 MRD.14: 6 residues within 4Å: Chain D: F.43, Y.57, H.59 Chain E: Q.9, L.42, H.59 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.42, D:F.43, D:F.43, D:F.43 Hydrogen bonds: E:Q.9, D:H.59 MRD.18: 6 residues within 4Å: Chain E: F.43, Y.57, H.59 Chain F: Q.9, L.42, H.59 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.42, E:F.43, E:F.43 Hydrogen bonds: F:Q.9, E:H.59 MRD.22: 6 residues within 4Å: Chain A: Q.9, L.42, H.59 Chain F: F.43, Y.57, H.59 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:F.43, F:F.43, F:F.43, A:L.42 Hydrogen bonds: F:H.59, A:Q.9

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 8 residues within 4Å: Chain A: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain B: S.2 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.6, A:Q.9 Hydrogen bonds: A:D.41, A:K.58 Water bridges: A:F.40, A:F.40, B:K.7, B:K.7 MPD.7: 9 residues within 4Å: Chain B: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain C: S.2, H.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.6, B:Q.9 Hydrogen bonds: B:D.41, B:K.58 Water bridges: B:F.40, C:S.2 MPD.8: 5 residues within 4Å: Chain A: L.33, Q.52 Chain B: Y.26, T.63, V.65 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.26 Water bridges: B:Y.26 Hydrogen bonds: A:Q.52 MPD.12: 9 residues within 4Å: Chain C: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain D: S.2, H.3 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.6, C:Q.9 Hydrogen bonds: C:D.41, C:K.58 Water bridges: C:F.40, C:F.40, D:S.2, D:M.4 MPD.15: 8 residues within 4Å: Chain D: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain E: S.2 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.6, D:Q.9 Hydrogen bonds: D:D.41, D:K.58 Water bridges: D:F.40 MPD.19: 9 residues within 4Å: Chain E: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain F: S.2, H.3 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.6, E:Q.9 Hydrogen bonds: E:D.41, E:K.58 Water bridges: E:F.40 MPD.23: 9 residues within 4Å: Chain A: S.2, H.3 Chain F: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:Y.6, F:Q.9 Hydrogen bonds: F:D.41, F:K.58 Water bridges: F:F.40, A:S.2

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

CL.3: 4 residues within 4Å: Chain A: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain E: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain F: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP

2 x GAI: GUANIDINE(Non-covalent)

GAI.4: 1 residues within 4Å: Chain A: Y.6 No protein-ligand interaction detected (PLIP) GAI.10: 2 residues within 4Å: Chain B: Y.26, G.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.30, B:G.30 Water bridges: B:Y.26, B:R.32

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

PEG.5: 9 residues within 4Å: Chain A: Y.26, L.27, T.62, T.63, V.65 Chain F: L.27, N.29, V.31, L.33 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:L.27, A:T.62, F:N.29 PEG.17: 9 residues within 4Å: Chain C: L.27, N.29, V.31, L.33 Chain D: Y.26, L.27, T.62, T.63, V.65 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.29, D:L.27, D:T.63 PEG.21: 9 residues within 4Å: Chain D: L.27, N.29, V.31, L.33 Chain E: Y.26, L.27, T.62, T.63, V.65 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:L.27, E:T.62, E:T.63, D:N.29 Water bridges: D:T.54 PEG.25: 9 residues within 4Å: Chain E: L.27, N.29, V.31, L.33 Chain F: Y.26, L.27, T.62, T.63, V.65 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:N.29, F:L.27, F:T.62 Water bridges: F:L.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanek, K.A. et al., Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-04-19

Peptides

RNA-binding protein Hfq: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

RNA-binding protein Hfq

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