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(-) Description

Title :  CRYSTAL STRUCTURE OF UBC9 (K48/K49A/E54A) COMPLEXED WITH FRAGMENT 1 (BIPHENOL FROM FRAGMENT COCKTAIL SCREEN)
 
Authors :  G. T. Lountos, W. M. Hewitt, K. Zlotkowski, S. Dahlhauser, L. B. Saunder D. Needle, J. E. Tropea, C. Zhan, G. Wei, B. Ma, R. Nussinov, J. S. Jr. Sch D. S. Waugh
Date :  07 Dec 15  (Deposition) - 27 Apr 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubc9, Fragment Drug Design, Sumoylation, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. M. Hewitt, G. T. Lountos, K. Zlotkowski, S. D. Dahlhauser, L. B. Saunders, D. Needle, J. E. Tropea, C. Zhan, G. Wei, B. Ma, R. Nussinov, D. S. Waugh, J. S. Schneekloth
Insights Into The Allosteric Inhibition Of The Sumo E2 Enzyme Ubc9.
Angew. Chem. Int. Ed. Engl. V. 55 5703 2016
PubMed-ID: 27038327  |  Reference-DOI: 10.1002/ANIE.201511351

(-) Compounds

Molecule 1 - SUMO-CONJUGATING ENZYME UBC9
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDN2405
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UBE2I, UBC9, UBCE9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUMO-PROTEIN LIGASE,UBIQUITIN CARRIER PROTEIN 9,UBIQUITIN CARRIER PROTEIN I,UBIQUITIN-CONJUGATING ENZYME E2 I,UBIQUITIN-PROTEIN LIGASE I,P18

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15VL1Ligand/Ion2-(2-HYDROXYPHENYL)PHENOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:42 , CYS A:43 , ALA A:44 , LYS A:59 , LEU A:60 , ARG A:61 , GLU A:78 , HOH A:412 , HOH A:457binding site for residue 5VL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F6V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:68 -Pro A:69
2Glu A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F6V)

(-) Exons   (0, 0)

(no "Exon" information available for 5F6V)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eeee................hhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f6v A   2 SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAP 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
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  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 5F6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F6V)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5f6v
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBC9_HUMAN | P63279: 1a3s 1kps 1z5q 1z5s 2grn 2gro 2grp 2grq 2grr 2o25 2pe6 2px9 2xwu 3a4s 3uin 3uio 3uip 4w5v 4y1l 5d2m 5f6d 5f6e 5f6u 5f6w 5f6x 5f6y 5fq2

(-) Related Entries Specified in the PDB File

5f6d 5f6e 5f6u 5f6w 5f6x 5f6y