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(-) Description

Title :  EBOLA VIRUS VP35 BOUND TO SMALL MOLECULE
 
Authors :  C. S. Brown, D. W. Leung, W. Xu, D. M. Borek, Z. Otwinowski, P. Ramanan, A. D. S. Peterson, J. M. Binning, G. K. Amarasinghe
Date :  08 Dec 12  (Deposition) - 19 Mar 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Interferon Inhibitor Domain, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Brown, M. S. Lee, D. W. Leung, T. Wang, W. Xu, P. Luthra, M. Anantpadma, R. S. Shabman, L. M. Melito, K. S. Macmillan, D. M. Borek Z. Otwinowski, P. Ramanan, A. J. Stubbs, D. S. Peterson, J. M. Binning, M. Tonelli, M. A. Olson, R. A. Davey, J. M. Ready, C. F. Basler, G. K. Amarasinghe
In Silico Derived Small Molecules Bind The Filovirus Vp35 Protein And Inhibit Its Polymerase Cofactor Activity.
J. Mol. Biol. V. 426 2045 2014
PubMed-ID: 24495995  |  Reference-DOI: 10.1016/J.JMB.2014.01.010

(-) Compounds

Molecule 1 - POLYMERASE COFACTOR VP35
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 215-340
    Gene: VP35
    Organism Common: ZEBOV
    Organism Scientific: EBOLA VIRUS
    Organism Taxid: 128952
    Strain: MAYINGA-76

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
11DE2Ligand/Ion3-{(2S)-2-(7-CHLORO-1,3-BENZODIOXOL-5-YL)-3-[(5-CHLOROTHIOPHEN-2-YL)CARBONYL]-4-HYDROXY-5-OXO-2,5-DIHYDRO-1H-PYRROL-1-YL}BENZOIC ACID
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
11DE1Ligand/Ion3-{(2S)-2-(7-CHLORO-1,3-BENZODIOXOL-5-YL)-3-[(5-CHLOROTHIOPHEN-2-YL)CARBONYL]-4-HYDROXY-5-OXO-2,5-DIHYDRO-1H-PYRROL-1-YL}BENZOIC ACID
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11DE1Ligand/Ion3-{(2S)-2-(7-CHLORO-1,3-BENZODIOXOL-5-YL)-3-[(5-CHLOROTHIOPHEN-2-YL)CARBONYL]-4-HYDROXY-5-OXO-2,5-DIHYDRO-1H-PYRROL-1-YL}BENZOIC ACID
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3GOL-1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:241 , GLN A:244 , LYS A:248 , LYS A:251 , PRO A:293 , ASP A:302 , ARG A:305 , DMS A:403 , HOH A:557 , GLN B:329BINDING SITE FOR RESIDUE 1DE A 401
2AC2SOFTWAREVAL A:314 , PRO A:315 , PRO A:316 , THR A:335 , HOH A:603BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREHIS A:296 , 1DE A:401 , HIS B:296 , GLN B:329BINDING SITE FOR RESIDUE DMS A 403
4AC4SOFTWAREHIS A:296 , GLN A:329 , HIS B:296 , 1DE B:401BINDING SITE FOR RESIDUE DMS A 404
5AC5SOFTWAREGLN A:329 , DMS A:404 , GLN B:241 , GLN B:244 , LYS B:248 , LYS B:251 , PRO B:293 , ASP B:302 , HOH B:550BINDING SITE FOR RESIDUE 1DE B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IBK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IBK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IBK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IBK)

(-) Exons   (0, 0)

(no "Exon" information available for 4IBK)

(-) 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh.ee......hhhh.eeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibk A 218 DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   227       237       247       257       267       277       287       297       307       317       327       337   


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhh.ee......hhhh.eeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibk B 217 PDISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI 340
                                   226       236       246       256       266       276       286       296       306       316       326       336
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  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 4IBK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IBK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IBK)

(-) Gene Ontology  (21, 21)

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  VP35_EBOZM | Q05127
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP35_EBOZM | Q05127: 3fke 3l25 3l26 3l27 3l28 3l29 4ibb 4ibc 4ibd 4ibe 4ibf 4ibg 4ibi 4ibj 4ije 4ijf 4ypi 4zta 4ztg 4zti

(-) Related Entries Specified in the PDB File

4ibb 4ibc 4ibd 4ibe 4ibf 4ibg 4ibh 4ibi 4ibj