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(-) Description

Title :  NATIVE HUMAN MANGANESE SUPEROXIDE DISMUTASE
 
Authors :  J. Azadmanesh, S. R. Trickel, G. E. O. Borgstahl
Date :  07 Apr 17  (Deposition) - 17 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Azadmanesh, S. R. Trickel, G. E. O. Borgstahl
Substrate-Analog Binding And Electrostatic Surfaces Of Huma Manganese Superoxide Dismutase.
J. Struct. Biol. V. 199 68 2017
PubMed-ID: 28461152  |  Reference-DOI: 10.1016/J.JSB.2017.04.011

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 25-222
    Gene: SOD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2MN2Ligand/IonMANGANESE (II) ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:301binding site for residue MN A 201
2AC2SOFTWAREHIS A:2 , SER A:3 , HIS A:71 , HOH A:309 , HOH A:352 , HOH A:378binding site for residue PO4 A 202
3AC3SOFTWAREGLY A:12 , HOH A:344 , HOH A:365 , GLY B:85 , ASN B:182 , HOH B:426binding site for residue K A 203
4AC4SOFTWAREHIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:301binding site for residue MN B 201
5AC5SOFTWARELYS A:178 , HIS B:2 , SER B:3 , HIS B:71 , HOH B:354binding site for residue PO4 B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5VF9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VF9)

(-) Exons   (0, 0)

(no "Exon" information available for 5VF9)

(-) 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:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vf9 A   0 MKHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 198
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         


Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vf9 B   0 MKHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 198
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
   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 5VF9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VF9)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SODM_HUMAN | P04179: 1ap5 1ap6 1em1 1ja8 1luv 1luw 1msd 1n0j 1n0n 1pl4 1pm9 1qnm 1szx 1var 1xdc 1xil 1zsp 1zte 1zuq 2adp 2adq 2gds 2p4k 2qka 2qkc 3c3s 3c3t 5t30

(-) Related Entries Specified in the PDB File

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