SMTL ID : 5szd.3 (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-12-mer

Ligands

13 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: 1 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:H.3, F:K.58 Hydrophobic interactions: F:Y.6, F:Q.9 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: 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.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: 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.43, D:F.43, D:F.43, E:Y.6, E:L.42 Hydrogen bonds: D:H.59, E:Q.9 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 E, 2 interactions with chain F Hydrophobic interactions: E:F.43, F:L.42 Hydrogen bonds: E:H.59, F:Q.9 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 MRD.20: 6 residues within 4Å: Chain G: F.43, Y.57, H.59 Chain H: Q.9, L.42, H.59 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:F.43, G:F.43, G:F.43, H:L.42 Hydrogen bonds: G:H.59, H:Q.9 MRD.25: 6 residues within 4Å: Chain H: F.43, Y.57, H.59 Chain I: Q.9, L.42, H.59 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:F.43, H:F.43, I:L.42 Hydrogen bonds: H:H.59, I:Q.9 MRD.30: 6 residues within 4Å: Chain I: F.43, Y.57, H.59 Chain J: Q.9, L.42, H.59 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:F.43, I:F.43, I:F.43, J:L.42 Hydrogen bonds: I:H.59, J:Q.9 MRD.33: 6 residues within 4Å: Chain J: F.43, Y.57, H.59 Chain K: Q.9, L.42, H.59 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:F.43, J:F.43, J:F.43, K:L.42 Hydrogen bonds: J:H.59, K:Q.9 MRD.37: 6 residues within 4Å: Chain K: F.43, Y.57, H.59 Chain L: Q.9, L.42, H.59 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:L.42, K:F.43, K:F.43 Hydrogen bonds: L:Q.9, K:H.59 MRD.41: 6 residues within 4Å: Chain G: Q.9, L.42, H.59 Chain L: F.43, Y.57, H.59 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain G Hydrophobic interactions: L:F.43, L:F.43, L:F.43, G:L.42 Hydrogen bonds: L:H.59, G:Q.9

12 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 MPD.21: 8 residues within 4Å: Chain G: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain H: S.2 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:Y.6, G:Q.9 Hydrogen bonds: G:D.41, G:K.58 Water bridges: G:F.40, G:F.40, H:K.7, H:K.7 MPD.26: 9 residues within 4Å: Chain H: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain I: S.2, H.3 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:Y.6, H:Q.9 Hydrogen bonds: H:D.41, H:K.58 Water bridges: H:F.40, I:S.2 MPD.27: 5 residues within 4Å: Chain G: L.33, Q.52 Chain H: Y.26, T.63, V.65 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:Y.26 Water bridges: H:Y.26 Hydrogen bonds: G:Q.52 MPD.31: 9 residues within 4Å: Chain I: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain J: S.2, H.3 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:Y.6, I:Q.9 Hydrogen bonds: I:D.41, I:K.58 Water bridges: I:F.40, I:F.40, J:S.2, J:M.4 MPD.34: 8 residues within 4Å: Chain J: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain K: S.2 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.6, J:Q.9 Hydrogen bonds: J:D.41, J:K.58 Water bridges: J:F.40 MPD.38: 9 residues within 4Å: Chain K: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 Chain L: S.2, H.3 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:Y.6, K:Q.9 Hydrogen bonds: K:D.41, K:K.58 Water bridges: K:F.40 MPD.42: 9 residues within 4Å: Chain G: S.2, H.3 Chain L: Y.6, Q.9, E.10, F.40, D.41, L.42, K.58 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain G Hydrophobic interactions: L:Y.6, L:Q.9 Hydrogen bonds: L:D.41, L:K.58 Water bridges: L:F.40, G:S.2

8 x GAI: GUANIDINE(Non-covalent)

GAI.4: 5 residues within 4Å: Chain A: N.29, G.30 Chain F: N.29 Chain I: L.42 Chain J: Y.6 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrogen bonds: J:Y.6, J:Y.6, J:Y.6, 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: 3 residues within 4Å: Chain B: N.29, G.30 Chain K: Y.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.29 GAI.11: 4 residues within 4Å: Chain C: N.29, G.30 Chain K: L.42 Chain L: Y.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain L Hydrogen bonds: C:N.29, C:N.29, L:Y.6 GAI.16: 4 residues within 4Å: Chain E: N.29, G.30 Chain G: L.42 Chain H: Y.6 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:N.29, E:N.29, H:Y.6, H:Y.6 GAI.19: 4 residues within 4Å: Chain F: N.29, G.30 Chain H: L.42 Chain I: Y.6 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 1 interactions with chain I Water bridges: E:N.29 Hydrogen bonds: F:N.29, F:N.29, I:Y.6 GAI.23: 3 residues within 4Å: Chain D: N.29, G.30 Chain G: Y.6 No protein-ligand interaction detected (PLIP) GAI.29: 2 residues within 4Å: Chain H: Y.26, G.30 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:G.30, H:G.30 Water bridges: H:Y.26, H:R.32

7 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 CL.22: 5 residues within 4Å: Chain D: Y.26 Chain G: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain E: Y.26 Chain H: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain F: Y.26 Chain I: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain A: Y.26 Chain J: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain B: Y.26 Chain K: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP CL.43: 5 residues within 4Å: Chain C: Y.26 Chain L: M.4, P.5, Y.6, K.7 Ligand excluded by PLIP

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

PEG.24: 9 residues within 4Å: Chain G: Y.26, L.27, T.62, T.63, V.65 Chain L: L.27, N.29, V.31, L.33 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:L.27, G:T.62, L:N.29 PEG.36: 9 residues within 4Å: Chain I: L.27, N.29, V.31, L.33 Chain J: Y.26, L.27, T.62, T.63, V.65 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:L.27, J:T.63, I:N.29 PEG.40: 9 residues within 4Å: Chain J: L.27, N.29, V.31, L.33 Chain K: Y.26, L.27, T.62, T.63, V.65 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:L.27, K:T.62, K:T.63, J:N.29 Water bridges: J:T.54 PEG.44: 9 residues within 4Å: Chain K: L.27, N.29, V.31, L.33 Chain L: Y.26, L.27, T.62, T.63, V.65 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:L.27, L:T.62, K:N.29 Water bridges: L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

RNA-binding protein Hfq

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