SMTL ID : 9avr.1

Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: F.52, K.54, P.55, S.56, Q.59, Q.77, S.78, G.79, T.80, G.81, K.82, T.83, E.183, A.214, G.335, D.337, Q.339, R.362, R.365, F.366 Ligands: MG.2 33 PLIP interactions: 33 interactions with chain A Hydrogen bonds: A:K.54, A:S.56, A:Q.59, A:G.79, A:T.80, A:G.81, A:K.82, A:K.82, A:K.82, A:T.83, A:T.83, A:T.83, A:G.335, A:D.337, A:R.362, A:R.362, A:R.365, A:R.365 Water bridges: A:Y.50, A:E.53, A:E.53, A:K.82, A:A.84, A:Q.115, A:Q.115, A:E.183, A:E.183, A:A.214, A:H.358 Salt bridges: A:R.365 pi-Stacking: A:F.52, A:F.52, A:F.366

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.83, D.182, E.183 Ligands: ANP.1 No protein-ligand interaction detected (PLIP)

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 3 residues within 4Å: Chain A: T.215, M.216, Y.391 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: K.284, Y.347 Ligand excluded by PLIP

1 x 01: silvestrol

01.5: 15 residues within 4Å: Chain A: R.110, P.159, G.160, F.163, D.164, N.167, Q.195, D.198, I.199, G.304, R.311 Chain B: A.5, G.6, A.7, G.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.163, A:F.163, A:Q.195, A:Q.195, A:D.198 Hydrogen bonds: A:Q.195 Water bridges: A:R.110, A:N.167 Salt bridges: A:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naineni, S.K. et al., Protein-RNA interactions mediated by silvestrol-insight into a unique molecular clamp. Nucleic Acids Res. (2024)

Release Date

2024-10-23

Peptides

Eukaryotic initiation factor 4A-I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Eukaryotic initiation factor 4A-I

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