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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN WD REPEAT DOMAIN 5 WITH COMPOUND MM-402
 
Authors :  H. Karatas, E. C. Townsend, Y. Chen, D. Bernard, F. Cao, L. Liu, M. Lei, Y. S. Wang
Date :  15 Aug 12  (Deposition) - 19 Feb 14  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Mll1, Histone Methyltransferase, Wd40, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Karatas, Y. Li, L. Liu, J. Ji, S. Lee, Y. Chen, J. Yang, L. Huang, D. Bernard, J. Xu, E. C. Townsend, F. Cao, X. Ran, X. Li, B. Wen, D. Sun, J. A. Stuckey, M. Lei, Y. Dou, S. Wang
Discovery Of A Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (Mm-589) Targeting The Wd Repeat Domain 5 Protein (Wdr5)-Mixed Lineage Leukemia (Mll) Protein-Protein Interaction.
J. Med. Chem. 2017
PubMed-ID: 28603984  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01796

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-334
    Gene: WDR5, BIG3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: WDR5, BMP2-INDUCED 3-KB GENE PROTEIN
 
Molecule 2 - MM-402
    Chains: E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
10XQ1Mod. Amino Acid(2R)-2,8-DIAMINO-2-METHYLOCTANOIC ACID
2ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3ALQ1Mod. Amino Acid2-METHYL-PROPIONIC ACID
4PG91Mod. Amino AcidD-PHENYLGLYCINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:47 , SER A:49 , GLY A:89 , ILE A:90 , SER A:91 , ASP A:107 , PHE A:133 , PHE A:149 , TYR A:260 , CYS A:261 , PHE A:263 , HOH E:101 , HOH E:102BINDING SITE FOR CHAIN E OF MM-402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GMB)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4gmba_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee....eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee.......eeeeee......eeeee...eeeeee....eeeeee...........eeee.....eeee......eeeee.....eeeee......eeeeee.....eeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gmb A  28 PTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4gmb E   1 xxRax   5
                            || ||
                            1-ALQ
                             2-0XQ
                               4-ABA
                                5-PG9
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        WDR5_HUMAN | P61964: 2cnx 2co0 2g99 2g9a 2gnq 2h13 2h14 2h68 2h6k 2h6n 2h6q 2h9l 2h9m 2h9n 2h9p 2o9k 3eg6 3emh 3mxx 3n0d 3n0e 3p4f 3psl 3smr 3ur4 3uvk 3uvl 3uvm 3uvn 3uvo 4a7j 4cy1 4cy2 4erq 4ery 4erz 4es0 4esg 4ewr 4gm3 4gm8 4gm9 4ia9 4o45 4ql1 4qqe 4y7r 5eal 5eam 5eap 5ear 5m23 5m25 5sxm 5vfc

(-) Related Entries Specified in the PDB File

4gm3 4gm8 4gm9