SMTL ID : 5szd.1 (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

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

MRD.1: 5 residues within 4Å: Chain A: F.43, Y.57, H.59 Chain B: Q.9, L.42 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.2: 8 residues within 4Å: Chain A: H.3 Chain F: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:Y.6, F:Q.9 Hydrogen bonds: F:K.58, A:H.3 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.9: 6 residues within 4Å: Chain C: F.43, Y.57, H.59 Chain D: Q.9, L.42, H.59 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.43, C:F.43, C:F.43, D:L.42 Hydrogen bonds: C:H.59, D:Q.9 MRD.12: 7 residues within 4Å: Chain D: F.43, Y.57, H.59 Chain E: Y.6, Q.9, L.42, H.59 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:Y.6, E:L.42, D:F.43, D:F.43, D:F.43 Hydrogen bonds: E:Q.9, D:H.59 MRD.14: 6 residues within 4Å: Chain E: F.43, Y.57, H.59 Chain F: Q.9, L.42, H.59 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:L.42, E:F.43 Hydrogen bonds: F:Q.9, E:H.59 MRD.17: 6 residues within 4Å: Chain A: Q.9, L.42, H.59 Chain F: F.43, Y.57, H.59 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:L.42, F:F.43, F:F.43, F:F.43 Hydrogen bonds: A:Q.9, F:H.59

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

MPD.3: 6 residues within 4Å: Chain A: Q.9, E.10, F.40, D.41, L.42, K.58 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.9, A:E.10 Hydrogen bonds: A:D.41, A:K.58 MPD.7: 7 residues within 4Å: Chain B: Q.9, E.10, F.40, D.41, L.42, K.58 Chain C: P.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.9 Hydrogen bonds: B:D.41, B:K.58, C:P.5 Water bridges: B:L.42 MPD.10: 6 residues within 4Å: Chain C: Q.9, E.10, F.40, D.41, L.42, K.58 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.9, C:E.10, C:E.10 Hydrogen bonds: C:D.41, C:K.58 MPD.13: 6 residues within 4Å: Chain D: Q.9, E.10, F.40, D.41, L.42, K.58 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Q.9, D:E.10 Hydrogen bonds: D:D.41, D:K.58 MPD.15: 6 residues within 4Å: Chain E: Q.9, E.10, F.40, D.41, L.42, K.58 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Q.9, E:E.10, E:E.10 Hydrogen bonds: E:D.41, E:K.58 Water bridges: E:L.42

6 x GAI: GUANIDINE(Non-covalent)

GAI.4: 3 residues within 4Å: Chain A: N.29, G.30 Chain F: N.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.29, A:N.29 GAI.5: 2 residues within 4Å: Chain A: Y.6 Chain F: L.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.6 GAI.8: 2 residues within 4Å: Chain B: N.29, G.30 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.29 GAI.11: 2 residues within 4Å: Chain C: N.29, G.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.29, C:N.29 GAI.16: 2 residues within 4Å: Chain E: N.29, G.30 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Water bridges: D:N.29 Hydrogen bonds: E:N.29, E:N.29 GAI.19: 2 residues within 4Å: Chain F: N.29, G.30 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.29, F:N.29 Water bridges: E:N.29

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

CL.18: 4 residues within 4Å: Chain F: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP

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
A

B
B

C
C

D
D

E
E

F
F

RNA-binding protein Hfq

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