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(-) Description

Title :  ZINC FINGERS OF KDM2B
 
Authors :  K. Liu, C. Xu, W. Tempel, J. R. Walker, C. H. Arrowsmith, C. Bountra, A. M. J. Min, Structural Genomics Consortium (Sgc)
Date :  20 Dec 13  (Deposition) - 16 Apr 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cxxc Zinc Finger, Ring Zinc Finger, Structural Genomics, Structural Genomics Consortium, Sgc, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Liu, C. Xu, W. Tempel, J. R. Walker, C. H. Arrowsmith, C. Bountra, A. M. Edwards, J. Min, Structural Genomics Consortium (Sgc)
Zinc Fingers Of Kdm2B
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 2B
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 607-723
    Gene: KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CXXC-TYPE ZINC FINGER PROTEIN 2, F-BOX AND LEUCINE-RICH REPEAT PROTEIN 10, F-BOX PROTEIN FBL10, F-BOX/LRR-REPEAT PROTEIN 10, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1B, JUMONJI DOMAIN-CONTAINING EMSY-INTERACTOR METHYLTRANSFERASE MOTIF PROTEIN, PROTEIN JEMMA, PROTEIN-CONTAINING CXXC DOMAIN 2, [HISTONE-H3]-LYSINE- 36 DEMETHYLASE 1B

 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, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1UNX14Ligand/IonUNKNOWN ATOM OR ION
2ZN12Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1UNX6Ligand/IonUNKNOWN ATOM OR ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1UNX4Ligand/IonUNKNOWN ATOM OR ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1UNX4Ligand/IonUNKNOWN ATOM OR ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:613 , CYS A:616 , CYS A:619 , CYS A:651BINDING SITE FOR RESIDUE ZN A 2001
02AC2SOFTWARECYS A:624 , CYS A:627 , CYS A:630 , CYS A:646BINDING SITE FOR RESIDUE ZN A 2002
03AC3SOFTWARECYS A:662 , CYS A:665 , HIS A:696 , CYS A:699BINDING SITE FOR RESIDUE ZN A 2003
04AC4SOFTWARECYS A:688 , CYS A:691 , CYS A:719 , CYS A:722BINDING SITE FOR RESIDUE ZN A 2004
05AC5SOFTWARECYS B:613 , CYS B:616 , CYS B:619 , CYS B:651BINDING SITE FOR RESIDUE ZN B 2001
06AC6SOFTWARECYS B:624 , CYS B:627 , CYS B:630 , CYS B:646BINDING SITE FOR RESIDUE ZN B 2002
07AC7SOFTWARECYS B:662 , CYS B:665 , HIS B:696 , CYS B:699BINDING SITE FOR RESIDUE ZN B 2003
08AC8SOFTWARECYS B:688 , CYS B:691 , CYS B:719 , CYS B:722BINDING SITE FOR RESIDUE ZN B 2004
09AC9SOFTWARECYS C:613 , CYS C:616 , CYS C:619 , CYS C:651BINDING SITE FOR RESIDUE ZN C 2001
10BC1SOFTWARECYS C:624 , CYS C:627 , CYS C:630 , CYS C:646BINDING SITE FOR RESIDUE ZN C 2002
11BC2SOFTWARECYS C:662 , CYS C:665 , HIS C:696 , CYS C:699BINDING SITE FOR RESIDUE ZN C 2003
12BC3SOFTWARECYS C:688 , CYS C:691 , CYS C:719 , CYS C:722BINDING SITE FOR RESIDUE ZN C 2004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O64)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O64)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O64)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O64)

(-) Exons   (0, 0)

(no "Exon" information available for 4O64)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....hhhhhhhhhhh........hhhhh...................hhhhh.hhhhhhhh..eee.....eehhhhh.......ee......eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4o64 A 608 RRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCN 723
                                   617       627       637       647       657       667       677       687       697       707       717      


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....hhhhhhhhhhh........hhhhh.........................hhhhhhhh..eee.....eehhhhh......ee......eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4o64 B 608 RRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKSEGVVNDELPNCWECPKCN 723
                                   617       627       637       647       657       667       677       687       697     ||708       718     
                                                                                                                         703|                  
                                                                                                                          705                  


Chain C from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....hhhhhhhhhhh........hhhhh...................hhhhh.hhhhhhhh..eee.....eehhhhh.......ee......eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4o64 C 608 RRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCN 723
                                   617       627       637       647       657       667       677       687       697       707       717
   Legend:   → Mismatch (orange background)
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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 4O64)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O64)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O64)

(-) Gene Ontology  (35, 35)

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  4o64
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  KDM2B_HUMAN | Q8NHM5
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        KDM2B_HUMAN | Q8NHM5: 5jh5

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