9AVR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.197 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AG8Click on this verticalbar to view detailsBest fitted ANPClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

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

Bhatt, G.B.Naineni, S.K.Nagar, B.N.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-I406Homo sapiensMutation(s): 0 
Gene Names: EIF4A1DDX2AEIF4A
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P60842 (Homo sapiens)
Explore P60842 
Go to UniProtKB:  P60842
PHAROS:  P60842
GTEx:  ENSG00000161960 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60842
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AG8 (Subject of Investigation/LOI)
Query on A1AG8

Download Ideal Coordinates CCD File 
G [auth B]silvestrol
C34 H38 O13
GVKXFVCXBFGBCD-QKDMMWSPSA-N
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.48α = 90
b = 84.295β = 90
c = 88.412γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AG8Click on this verticalbar to view detailsBest fitted ANPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release