SMTL ID : 5sze.1 (1 other biounit)

Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x U- U- U: RNA (5'-R(P*UP*UP*U)-3')(Non-covalent)

U-U-U.1: 12 residues within 4Å: Chain A: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Chain E: H.3, M.4, P.5, Y.6 Protein-ligand interaction information (PLIP) not available U-U-U.4: 12 residues within 4Å: Chain B: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Chain F: H.3, M.4, P.5, Y.6 Protein-ligand interaction information (PLIP) not available U-U-U.7: 12 residues within 4Å: Chain C: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Chain D: H.3, M.4, P.5, Y.6 Protein-ligand interaction information (PLIP) not available U-U-U.10: 12 residues within 4Å: Chain B: H.3, M.4, P.5, Y.6 Chain D: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Protein-ligand interaction information (PLIP) not available U-U-U.13: 12 residues within 4Å: Chain C: H.3, M.4, P.5, Y.6 Chain E: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Protein-ligand interaction information (PLIP) not available U-U-U.16: 12 residues within 4Å: Chain A: H.3, M.4, P.5, Y.6 Chain F: K.7, E.10, N.14, R.17, K.18, R.38, S.39, F.40 Protein-ligand interaction information (PLIP) not available

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

MRD.2: 5 residues within 4Å: Chain A: F.43, Y.57, H.59 Chain E: Q.9, L.42 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.43, A:F.43, A:F.43, E:L.42 Hydrogen bonds: A:H.59, E:Q.9 MRD.5: 5 residues within 4Å: Chain B: F.43, Y.57, H.59 Chain F: Q.9, L.42 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:F.43, B:F.43, B:F.43, F:L.42 Hydrogen bonds: B:H.59, F:Q.9 MRD.8: 5 residues within 4Å: Chain C: F.43, Y.57, H.59 Chain D: Q.9, L.42 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.11: 5 residues within 4Å: Chain B: Q.9, L.42 Chain D: F.43, Y.57, H.59 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.42, D:F.43, D:F.43, D:F.43 Hydrogen bonds: B:Q.9, D:H.59 MRD.14: 5 residues within 4Å: Chain C: Q.9, L.42 Chain E: F.43, Y.57, H.59 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:F.43, E:F.43, E:F.43, C:L.42 Hydrogen bonds: E:H.59, C:Q.9 MRD.17: 5 residues within 4Å: Chain A: Q.9, L.42 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

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

PEG.3: 8 residues within 4Å: Chain A: Y.26, L.27, T.62, T.63, V.65 Chain F: L.27, N.29, V.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:T.62, F:N.29 PEG.6: 8 residues within 4Å: Chain B: Y.26, L.27, T.62, T.63, V.65 Chain D: L.27, N.29, V.31 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.29, B:T.62 PEG.9: 8 residues within 4Å: Chain C: Y.26, L.27, T.62, T.63, V.65 Chain E: L.27, N.29, V.31 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:T.62, E:N.29 PEG.12: 8 residues within 4Å: Chain C: L.27, N.29, V.31 Chain D: Y.26, L.27, T.62, T.63, V.65 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.29, D:T.62 PEG.15: 8 residues within 4Å: Chain A: L.27, N.29, V.31 Chain E: Y.26, L.27, T.62, T.63, V.65 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.29, E:T.62 PEG.18: 8 residues within 4Å: Chain B: L.27, N.29, V.31 Chain F: Y.26, L.27, T.62, T.63, V.65 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:T.62, B:N.29

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

2017-04-12

Peptides

RNA-binding protein Hfq: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

RNA-binding protein Hfq

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