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(-) Description

Title :  CRYSTAL STRUCTURE OF ZEBRAFISH ALKBH5 IN COMPLEX WITH SUCCINIC ACID
 
Authors :  C. He, W. Chen, L. Zhang
Date :  21 Nov 13  (Deposition) - 19 Feb 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Chen, L. Zhang, G. Zheng, Y. Fu, Q. Ji, F. Liu, H. Chen, C. He
Crystal Structure Of The Rna Demethylase Alkbh5 From Zebrafish.
Febs Lett. V. 588 892 2014
PubMed-ID: 24561204  |  Reference-DOI: 10.1016/J.FEBSLET.2014.02.021

(-) Compounds

Molecule 1 - RNA DEMETHYLASE ALKBH5
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 38-287
    Gene: ALKBH5
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2SIN2Ligand/IonSUCCINIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SIN1Ligand/IonSUCCINIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:135 , ASP A:137 , HIS A:197 , SIN A:301 , HOH A:414 , HOH A:634BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREASN A:124 , TYR A:126 , ILE A:132 , HIS A:135 , HIS A:197 , ILE A:199 , ARG A:208 , VAL A:210 , ILE A:212 , MN A:300 , HOH A:414 , HOH A:455 , HOH A:634BINDING SITE FOR RESIDUE SIN A 301
3AC3SOFTWAREHIS B:135 , ASP B:137 , HIS B:197 , SIN B:301 , HOH B:417 , HOH B:632BINDING SITE FOR RESIDUE MN B 300
4AC4SOFTWAREASN B:124 , TYR B:126 , ILE B:132 , HIS B:135 , HIS B:197 , ILE B:199 , ARG B:208 , VAL B:210 , ILE B:212 , MN B:300 , HOH B:417 , HOH B:443 , HOH B:488 , HOH B:632BINDING SITE FOR RESIDUE SIN B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:144 -Pro A:145
2Lys A:166 -Pro A:167
3Arg B:144 -Pro B:145
4Lys B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NPM)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee...ee..ee.........hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee...ee....ee....eeeee....eeeehhhhhhh..eeehhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4npm A   4 EYEERRDAEARRVKSGIKQASIFTLEECARIEAKIDEVVAKADKGLYREHTVDRAPLRNKYFFGEGYTQERLYSKGEVDDIPDWVHELVIDRLVTHGVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFLFKPIRVSEPVLHLPVRRGSVTVLSGYAADDITHCIRPQDIKERRAVIILRKTRADAPRLD 224
                                    13        23        33        43        53        63       |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
                                                                                              71|                                                                                                                                             
                                                                                               83                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhheeee...hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee...ee..ee.........hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee...ee....ee....eeeee....eeeehhhhhhh..eeehhhhh...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4npm B   9 RDAEARRVKSGIKQASIFTLEECARIEAKIDEVVAKADKGLYREHTVDRAPLRNKYFFGEGYTQERLYSKGEVDDIPDWVHELVIDRLVTHGVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFLFKPIRVSEPVLHLPVRRGSVTVLSGYAADDITHCIRPQDIKERRAVIILRKTRADAPRL 223
                                    18        28        38        48        58        68  ||    89        99       109       119       129       139       149       159       169       179       189       199       209       219    
                                                                                         71|                                                                                                                                            
                                                                                          83
   Legend:   → Mismatch (orange background)
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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 4NPM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        ALKB5_DANRE | Q08BA6: 4npl

(-) Related Entries Specified in the PDB File

4npl