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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN WDR5 IN COMPLEX WITH COMPOUND 9D
 
Authors :  A. Dong, L. Dombrovski, D. Smil, M. Getlik, Y. Bolshan, J. R. Walker, G. Senisterra, G. Poda, R. Al-Awar, M. Schapira, M. Vedadi, C. Bountra A. M. Edwards, C. H. Arrowsmith, P. J. Brown, H. Wu, Structural Genomi Consortium (Sgc)
Date :  16 Oct 15  (Deposition) - 04 Nov 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Wdr5, Compound 9D, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription - Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Dombrovski, A. Dong, D. Smil, M. Getlik, Y. Bolshan, J. R. Walker, G. Senisterra, G. Poda, R. Al-Awar, M. Schapira, M. Vedadi, C. Bountra A. M. Edwards, C. H. Arrowsmith, P. J. Brown, H. Wu, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Wdr5 In Complex With Compound 9D
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)V2RPRARE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-334
    Gene: WDR5, BIG3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BMP2-INDUCED 3-KB GENE PROTEIN

 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  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
15MQ2Ligand/IonN-[5-(2,3-DIHYDRO-1-BENZOFURAN-7-YL)-2-(4-METHYLPIPERAZIN-1-YL)PHENYL]-3-METHYLBENZAMIDE
2EDO19Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
4UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
15MQ1Ligand/IonN-[5-(2,3-DIHYDRO-1-BENZOFURAN-7-YL)-2-(4-METHYLPIPERAZIN-1-YL)PHENYL]-3-METHYLBENZAMIDE
2EDO9Ligand/Ion1,2-ETHANEDIOL
3SO4-1Ligand/IonSULFATE ION
4UNX2Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
15MQ1Ligand/IonN-[5-(2,3-DIHYDRO-1-BENZOFURAN-7-YL)-2-(4-METHYLPIPERAZIN-1-YL)PHENYL]-3-METHYLBENZAMIDE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
4UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:49 , SER A:50 , ALA A:65 , ILE A:90 , SER A:91 , PHE A:133 , SER A:175 , TYR A:191 , CYS A:261 , ILE A:305 , EDO A:406 , HOH A:575 , HOH A:578binding site for residue 5MQ A 401
02AC2SOFTWARELYS A:123 , VAL A:158 , LYS A:159 , HOH A:560 , HOH A:705binding site for residue EDO A 402
03AC3SOFTWARELYS A:165 , THR A:200 , ALA A:201binding site for residue EDO A 403
04AC4SOFTWARELYS A:70 , PHE A:79 , HOH A:501binding site for residue EDO A 404
05AC5SOFTWARETHR A:40 , LEU A:206 , GLY A:299 , THR A:301 , ASP A:324 , THR A:326 , LYS A:328binding site for residue EDO A 405
06AC6SOFTWAREASP A:107 , PHE A:133 , 5MQ A:401 , HOH A:514binding site for residue EDO A 406
07AC7SOFTWAREPHE A:79 , LYS A:81 , THR A:82binding site for residue EDO A 407
08AC8SOFTWAREASP A:98 , ASN A:100 , HOH A:590 , LYS B:38binding site for residue EDO A 408
09AC9SOFTWARETYR A:260 , ASP A:302 , GLU A:322 , HOH A:542binding site for residue EDO A 409
10AD1SOFTWARETYR A:228 , LYS A:250 , GLN A:289 , HOH A:507 , HOH A:535binding site for residue EDO A 410
11AD2SOFTWARESER B:49 , SER B:50 , ALA B:65 , ILE B:90 , SER B:91 , PHE B:133 , SER B:175 , TYR B:191 , CYS B:261 , ILE B:305 , EDO B:410 , HOH B:511 , HOH B:583 , HOH B:666binding site for residue 5MQ B 401
12AD3SOFTWARELYS B:123 , THR B:124 , HOH B:501 , HOH B:516 , HOH B:647binding site for residue SO4 B 402
13AD4SOFTWARETYR B:228 , LEU B:240 , LYS B:250 , GLN B:289 , HOH B:519binding site for residue EDO B 403
14AD5SOFTWARESER A:129 , TYR B:260 , ASP B:302 , GLU B:322 , HOH B:669 , HOH B:721binding site for residue EDO B 404
15AD6SOFTWARETHR B:40 , LEU B:206 , GLY B:299 , THR B:301 , ASP B:324 , THR B:326 , LYS B:328 , HOH B:555 , HOH B:571 , HOH B:682binding site for residue EDO B 405
16AD7SOFTWAREALA B:42 , GLY B:43 , LYS B:70 , PHE B:79 , SER B:202 , HOH B:586binding site for residue EDO B 406
17AD8SOFTWAREPHE B:39 , ALA B:74 , TYR B:75 , HOH B:547binding site for residue EDO B 407
18AD9SOFTWARESER B:223 , PRO B:224 , ASN B:225 , TYR B:228 , HOH B:519 , HOH B:534 , HOH B:695binding site for residue EDO B 408
19AE1SOFTWAREPHE B:79 , LYS B:81 , THR B:82 , HOH B:707binding site for residue EDO B 409
20AE2SOFTWAREASP B:107 , PHE B:133 , 5MQ B:401binding site for residue EDO B 410
21AE3SOFTWARELYS B:123 , VAL B:158 , LYS B:159binding site for residue EDO B 411
22AE4SOFTWARELEU B:143 , ILE B:155 , LYS B:165 , THR B:200 , ALA B:201binding site for residue EDO B 412

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EAR)

(-) 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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......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
                 5ear A  31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLINPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|      223       233       243       253       263       273       283       293       303       313       323       333 
                                                                                                                                                                                                             210|                                                                                                                        
                                                                                                                                                                                                              214                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeeee...eeeeee.....eeeeee...eeeeee....eeeeee...........eeee.....eeee......eeeee.....eeeee......eeeeee.....eeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ear B  31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210||     223       233       243       253       263       273       283       293       303       313       323       333 
                                                                                                                                                                                                              211|                                                                                                                       
                                                                                                                                                                                                               215
   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 5EAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric 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 4gmb 4ia9 4o45 4ql1 4qqe 4y7r 5eal 5eam 5eap 5m23 5m25 5sxm 5vfc

(-) Related Entries Specified in the PDB File

5eal 5eam 5eap