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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 :  04 Nov 15  (Deposition) - 07 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.61
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Strain: BL21(DE3)
    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 4E-BINDING PROTEIN 1
    Chains: B, D
    Engineered: YES
    Fragment: EIF4E BINDING SEQUENCE, UNP RESIDUES 51-64
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: NATURAL SEQUENCE FROM 4EBP
    Synonym: EIF4E-BINDING PROTEIN 1,PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY INSULIN 1,PHAS-I
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15PQ2Ligand/Ion3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-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
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15PQ1Ligand/Ion3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-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
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15PQ1Ligand/Ion3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-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  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:56 , MET A:101 , TRP A:102 , GLU A:103 , ARG A:157binding site for residue 5PQ A 301
2AC2SOFTWARETRP C:56 , GLN C:57 , MET C:101 , TRP C:102 , GLU C:103 , ARG C:157binding site for residue 5PQ C 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EKV)

(-) Sequences/Alignments

Asymmetric 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee.....hhhhheeeeeeeeehhhhhhhhh...........eeeeeee................eeeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh......eee.hhhhhh.....eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ekv A  31 PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATTKNRFVV 217
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    || 215  
                                                                                                                                                                                                        205|      
                                                                                                                                                                                                         211      


Chain B from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5ekv B  51 RIIYDRKFLMECRN  64
                                    60    


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee.......hhhhhheeeeeeeehhhhhhhhhhh.........eeeeeee...............eeeeeee......hhhhhhhhhhhhhhhh..hhhhhh.eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh......eeeeehhhhh..eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ekv C  36 KHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTANRFVV 217
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       213    
                                                                                                                                                                                                  204|    
                                                                                                                                                                                                   213    


Chain D 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
                 5ekv D  51 RIIYDRKFLMECRN  64
                                    60
   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 5EKV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (46, 55)

Asymmetric Unit(hide GO term definitions)

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  4EBP1_HUMAN | Q13541
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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
        4EBP1_HUMAN | Q13541: 1ej4 1ejh 1wkw 2jgb 2jgc 2v8w 2v8x 2v8y 3hxg 3hxi 3m93 3m94 3u7x 4ued 5bxv
        IF4E_HUMAN | P06730: 1ipb 1ipc 1wkw 2gpq 2v8w 2v8x 2v8y 2w97 3am7 3tf2 3u7x 4aza 4bea 4dt6 4dum 4tpw 4tqb 4tqc 4ued 5ehc 5ei3 5eir 5gw6 5t46

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