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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALKBH7 IN COMPLEX WITH N-OXALYLGLYCINE AND MN(II)
 
Authors :  G. Wang, Z. Chen
Date :  06 Jun 14  (Deposition) - 20 Aug 14  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Dioxygenase, Metal-Binding, Oxidoreductase, Programmed Necrosis, Fat Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wang, Q. He, C. Feng, Y. Liu, Z. Deng, X. Qi, W. Wu, P. Mei, Z. Chen
The Atomic Resolution Structure Of Human Alkb Homolog 7 (Alkbh7), A Key Protein For Programmed Necrosis And Fat Metabolism
J. Biol. Chem. V. 289 27924 2014
PubMed-ID: 25122757  |  Reference-DOI: 10.1074/JBC.M114.590505

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 7, MITOCHONDRIAL
    Chains: A, B, C
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 17-215
    Gene: ABH7, ALKBH7, SPATA11, UNQ6002/PRO34564
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 7, SPERMATOGENESIS CELL PROLIFERATION-RELATED PROTEIN, SPERMATOGENESIS-ASSOCIATED PROTEIN 11

 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, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2OGA2Ligand/IonN-OXALYLGLYCINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2OGA-1Ligand/IonN-OXALYLGLYCINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:121 , ASP A:123 , HIS A:177 , OGA A:301BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREHIS A:108 , HIS A:121 , TYR A:165 , HIS A:177 , ILE A:179 , ARG A:197 , SER A:199 , ARG A:203 , MN A:300 , HOH A:430BINDING SITE FOR RESIDUE OGA A 301
3AC3SOFTWAREHOH A:449 , HIS B:121 , ASP B:123 , HIS B:177 , HOH B:426BINDING SITE FOR RESIDUE MN B 300
4AC4SOFTWAREHIS C:121 , ASP C:123 , HIS C:177 , OGA C:302BINDING SITE FOR RESIDUE MN C 301
5AC5SOFTWAREILE C:70 , LEU C:110 , ILE C:118 , HIS C:121 , ASP C:123 , TYR C:165 , HIS C:177 , ARG C:197 , SER C:199 , ILE C:201 , ARG C:203 , MN C:301 , HOH C:457BINDING SITE FOR RESIDUE OGA C 302
6AC6SOFTWAREGLU A:189 , GLU B:189 , GLU C:189BINDING SITE FOR RESIDUE MN C 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QKF)

(-) 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:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...........eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeeeeeeee.........eeeeeee...eeeeeee......eeeeee....eeeeehhhhhheeeee.hhhh.ee..ee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qkf A  16 MWVRGSGPSVLSRLQDAAVVRPGFLSTAEEETLSRELEPELRRRRYEYDHWDAAIHGFRETEKSRWSEASRAILRRVQAAAFGPQTLLSSVHVLDLEARGYIKPHVDSIKFCGATIAGLSLLSPSVMRLVHTQEPGEWLELLLEPGSLYILRGSARYDFSHEILRDEESFFGERRIPRGRRISVICRSLP 206
                                    25        35        45        55        65        75        85        95   ||  106       116       126       136       146       156       166       176       186       196       206
                                                                                                              99|                                                                                                         
                                                                                                              101                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...........eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeeeeeeee.........eeeeeee...eeeeeee......eeeeee...eeeeeehhhhhheeeee......ee..ee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qkf B  16 MWVRGSGPSVLSRLQDAAVVRPGFLSTAEEETLSRELEPELRRRRYEYDHWDAAIHGFRETEKSRWSEASRAILRRVQAAAFGPQTLLSSVHVLDLEARGYIKPHVDSIKFCGATIAGLSLLSPSVMRLVHTQEPGEWLELLLEPGSLYILRGSARYDFSHEILRDEESFFGERRIPRGRRISVICRSLP 206
                                    25        35        45        55        65        75        85        95   ||  106       116       126       136       146       156       166       176       186       196       206
                                                                                                              99|                                                                                                         
                                                                                                              101                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...........eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeeeeeeee.........eeeeeee...eeeeeee......eeeeee...eeeeeehhhhhheeeee.hhhh.ee..ee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qkf C  16 MWVRGSGPSVLSRLQDAAVVRPGFLSTAEEETLSRELEPELRRRRYEYDHWDAAIHGFRETEKSRWSEASRAILRRVQAAAFGPQTLLSSVHVLDLEARGYIKPHVDSIKFCGATIAGLSLLSPSVMRLVHTQEPGEWLELLLEPGSLYILRGSARYDFSHEILRDEESFFGERRIPRGRRISVICRSLP 206
                                    25        35        45        55        65        75        85        95   ||  106       116       126       136       146       156       166       176       186       196       206
                                                                                                              99|                                                                                                         
                                                                                                              101
   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 4QKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB7_HUMAN | Q9BT30: 4qkb 4qkd

(-) Related Entries Specified in the PDB File

4qkb 4qkd