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(-) Description

Title :  CRYSTAL STRUCTURE OF WD REPEAT-CONTAINING PROTEIN 20
 
Authors :  H. Li, A. D. D'Andrea, N. Zheng
Date :  17 May 16  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Wdr20, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, K. S. Lim, H. Kim, T. R. Hinds, U. Jo, H. Mao, C. E. Weller, J. Sun, C. Chatterjee, A. D. D'Andrea, N. Zheng
Allosteric Activation Of Ubiquitin-Specific Proteases By Beta-Propeller Proteins Uaf1 And Wdr20.
Mol. Cell V. 63 249 2016
PubMed-ID: 27373336  |  Reference-DOI: 10.1016/J.MOLCEL.2016.05.031

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 20
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Gene: WDR20
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN DMR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:145 , LYS A:149binding site for residue SO4 A 601
2AC2SOFTWARESER A:229 , PRO A:230 , ASP A:231 , PHE A:234 , GLY A:274 , PHE A:291binding site for residue GOL A 602
3AC3SOFTWAREARG B:151 , SER B:170binding site for residue SO4 B 601
4AC4SOFTWAREPHE A:17 , THR A:18 , LYS A:529 , THR B:18 , LYS B:529binding site for residue GOL B 602
5AC5SOFTWAREARG B:145 , LYS B:149 , HOH B:705binding site for residue GOL B 603
6AC6SOFTWAREARG B:49 , CYS B:103 , THR B:153 , CYS B:154 , ASN B:224 , GLU B:225binding site for residue GOL B 604
7AC7SOFTWAREILE C:95 , GLN C:240 , GLY C:263 , GLY C:264 , LEU C:266 , GLU C:282binding site for residue GOL C 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K19)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Cys A:183 -Gly A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K19)

(-) Exons   (0, 0)

(no "Exon" information available for 5K19)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeeee.hhhh................eeeee......eeeeee...eeeeee..............eeee.....eeeeee...........eeeee....eeee.......eeee..........eeeeee......eeeeee...eeeeee...........eeeeeee..eeeeee....eeeeeee....eeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee............eeeeeeee...eeeeeeeehhhhh...ee...eeee.....eeeeee...eeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k19 A  11 NEIKTQFTTREGLYKLLPHSEYSRPNRVPFNSSNPVRVSFVNLNSGNGDRLCFNVGRELYFYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNHLTATAESVSLLVGFSAGQVQLIDPIKKETSKLFNEERLIDKSRVTCVKWVPGSESLFLVAHSSGNMYLYNVEHTCGTTAPHYQLLKQGESFAVHTCKTRNPLLKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSVELHGTMKSYFGGLLCVCWSPDGKYIVTGGEDDLVTVWSFVDCRVIARGHGHKSWVSVVAFDPYTTSVEEGDVTYRFGSVGQDTQLCLWDLTEDILFPVPLLEPLICKKIAHERLTVLIFLEDCIVTACQEGFICTWGRPGK 563
                                    20        30        40 ||     52   ||   64        74        84        94       104       114       124       134       144       154       164       174       184       194       204||     217       227       237       247       257       267       277       287       297       307       317     ||368       378       388 ||    527       537       547       557      
                                                          42|         56|                                                                                                                                               205|                                                                                                               323|                      390|                                           
                                                           45          59                                                                                                                                                209                                                                                                                365                       520                                           


Chain B from PDB  Type:PROTEIN  Length:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee.......................eeeee........eeeeee...eeeeee..............eeee.....eeeeee...........eeeee....eeee.......eeee..........eeeeee......eeeeee...eeeeee...........eeeeeee..eeeeee......eeeee....eeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.hhhh.eeeeeeee...eeeeeeeehhhhh...ee...eeee.....eeeeee...eeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k19 B  12 EIKTQFTTREGLYKLLPHSEYSRPNRVPFNSQGSNPVRVSFVNLNDQSGNGDRLCFNVGRELYFYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNHLTATAESVSLLVGFSAGQVQLIDPIKKETSKLFNEERLIDKSRVTCVKWVPGSESLFLVAHSSGNMYLYNVEHTCGTTAPHYQLLKQGESFAVHTCKTRNPLLKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSVELHGTMKSYFGGLLCVCWSPDGKYIVTGGEDDLVTVWSFVDCRVIARGHGHKSWVSVVAFDPYTTVTYRFGSVGQDTQLCLWDLTEDILFDVPLLEPLICKKIAHERLTVLIFLEDCIVTACQEGFICTWGRPGK 563
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   ||  214       224       234       244       254       264       274       284       294       304       314  ||   371       381       520       530       540       550       560   
                                                                                                                                                                                                                           205|                                                                                                         317|                     389|                                            
                                                                                                                                                                                                                            209                                                                                                          365                      519                                            


Chain C from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.eeeeee..............eeeee....eeeeee...eeeeee..............eeee.....eeeeee...........eeeee....eeee.......eeee..........eeeeee......eeeeee...eeeeee...........eeeeeee..eeeeee......eeeee....eeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeee.....eeeeee....eeeee....eeeeee......eeeeeee.....eeeeeee...eeeeeeehhhhhh..ee....eee.....eeeeee....eeeee...eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k19 C  12 EIKTQFTTREGLYKLLPHSEYSRPNRVPFNSNPVRVSFVNLNNGDRLCFNVGRELYFYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNHLTATAESVSLLVGFSAGQVQLIDPIKKETSKLFNEERLIDKSRVTCVKWVPGSESLFLVAHSSGNMYLYNVEHTCGTTAPHYQLLKQGESFAVHTCKTRNPLLKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSVELHGTMKSYFGGLLCVCWSPDGKYIVTGGEDDLVTVWSFVDCRVIARGHGHKSWVSVVAFDPYTTTYRFGSVGQDTQLCLWDLTEDILFVPLLEPLICKKIAHERLTVLIFLEDCIVTACQEGFICTW 558
                                    21        31        41||      54 ||     68        78        88        98       108       118       128       138       148       158       168       178       188       198      |211       221       231       241       251       261       271       281       291       301       311     ||369       379       389|      529       539       549         
                                                         42|        56|                                                                                                                                             205|                                                                                                         317|                    389|                                      
                                                          46         61                                                                                                                                              209                                                                                                          366                     520
   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 5K19)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K19)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K19)

(-) Gene Ontology  (1, 1)

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        WDR20_HUMAN | Q8TBZ3: 5k1c

(-) Related Entries Specified in the PDB File

5k16 5k1a 5k1b 5k1c