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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF EIF4E WITH NUCLEOTIDE MIMETIC INHIBITOR.
 
Authors :  M. W. Nowicki, M. D. Walkinshaw, P. M. Fischer
Date :  28 Oct 15  (Deposition) - 07 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Inhibitor, Translation, Eif4E (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Soukarieh, M. W. Nowicki, A. Bastide, T. Poyry, C. Jones, K. Dudek, G. Patwardhan, F. Meullenet, N. J. Oldham, M. D. Walkinshaw, A. E. Willis, P. M. Fischer
Design Of Nucleotide-Mimetic And Non-Nucleotide Inhibitors Of The Translation Initiation Factor Eif4E: Synthesis, Structural And Functional Characterisation.
Eur. J. Med. Chem. V. 124 200 2016
PubMed-ID: 27592390  |  Reference-DOI: 10.1016/J.EJMECH.2016.08.047

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11D
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Gene: EIF4E, EIF4EL1, EIF4F
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EIF4E,EIF-4F 25 KDA SUBUNIT,MRNA CAP-BINDING PROTEIN
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1
    Chains: B
    Engineered: YES
    Fragment: EIF4E BINDING SEQUENCE, UNP RESIDUES 634-647
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: COMMERCIAL SYNTHESIS
    Synonym: EIF-4G1,P220
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15NX1Ligand/Ion3-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-AZANYL-7-[(3-CHLOROPHENYL)METHYL]-6-OXIDANYLIDENE-1~{H}-PURIN-7-IUM-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYLAMINO]-4-OXIDANYL-CYCLOBUT-3-ENE-1,2-DIONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:56 , MET A:101 , TRP A:102 , GLU A:103 , ARG A:157 , TRP A:166 , THR A:203 , ALA A:204 , HOH A:405binding site for residue 5NX A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EHC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EHC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EHC)

(-) Exons   (0, 0)

(no "Exon" information available for 5EHC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh...eeeeeeeeeee......hhhhheeeeeeeeehhhhhhhhh...hhhhh....eeeeee...............eeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee......eeeeee....hhhhhhhhhhhhhhhh.......eeeeehhhhh.....eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ehc A  27 EVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATTKNRFVV 217
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       211      
                                                                                                                                                                                                           204|       
                                                                                                                                                                                                            210       


Chain B from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author ....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5ehc B 621 KKRYDREFLLGFQF 634
                                   630
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EHC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EHC)

(-) Gene Ontology  (39, 51)

Asymmetric/Biological Unit(hide GO term definitions)

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  IF4E_HUMAN | P06730
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  IF4G1_HUMAN | Q04637
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  IF4E_HUMAN | P06730
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IF4E_HUMAN | P06730: 1ipb 1ipc 1wkw 2gpq 2v8w 2v8x 2v8y 2w97 3am7 3tf2 3u7x 4aza 4bea 4dt6 4dum 4tpw 4tqb 4tqc 4ued 5ei3 5eir 5ekv 5gw6 5t46
        IF4G1_HUMAN | Q04637: 1lj2 1ug3 2w97 4aza 4f02 5ei3 5eir 5t46

(-) Related Entries Specified in the PDB File

2v8w 2V8W CONTAINS THE SAME PROTEIN WITH A DIFFERENT LIGAND AND PEPTIDE