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(-) Description

Title :  HUMAN PEROXIREDOXIN 5 WITH A FRAGMENT
 
Authors :  J. F. Guichou
Date :  17 Apr 13  (Deposition) - 23 Apr 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A  (2x)
Biol. Unit 5:  B,C  (1x)
Keywords :  Enzyme, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Aguirre, T. T. Brink, J. F. Guichou, O. Cala, I. Krimm
Comparing Binding Modes Of Analogous Fragments Using Nmr In Fragment-Based Drug Design: Application To Prdx5
Plos One V. 9 02300 2014
PubMed-ID: 25025339  |  Reference-DOI: 10.1371/JOURNAL.PONE.0102300

(-) Compounds

Molecule 1 - PEROXIREDOXIN-5, MITOCHONDRIAL
    Chains: A, B, C
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 54-214
    Gene: PRDX5, ACR1, SBBI10
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALU COREPRESSOR 1, ANTIOXIDANT ENZYME B166, AOEB166, LIVER TISSUE 2D-PAGE SPOT 71B, PLP, PEROXIREDOXIN V, PRX-V, PEROXISOMAL ANTIOXIDANT ENZYME, TPX TYPE VI, THIOREDOXIN PEROXIDASE PMP20, THIOREDOXIN REDUCTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): A  
Biological Unit 5 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CAQ2Ligand/IonCATECHOL
2DMS2Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CAQ1Ligand/IonCATECHOL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CAQ1Ligand/IonCATECHOL
2DMS1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CAQ-1Ligand/IonCATECHOL
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1CAQ2Ligand/IonCATECHOL
2DMS2Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1CAQ1Ligand/IonCATECHOL
2DMS1Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:40 , THR A:44 , PRO A:45 , GLY A:46 , CYS A:47 , ARG A:127 , HOH A:2106 , ALA C:64BINDING SITE FOR RESIDUE CAQ A 201
2AC2SOFTWAREPHE A:43 , SER A:48 , GLU A:83 , TRP A:84 , HIS A:88BINDING SITE FOR RESIDUE DMS A 202
3AC3SOFTWAREALA A:64 , PRO B:40 , THR B:44 , PRO B:45 , GLY B:46 , CYS B:47 , ARG B:127BINDING SITE FOR RESIDUE CAQ B 201
4AC4SOFTWAREVAL B:70 , GLY B:92 , LYS B:93 , ARG B:95BINDING SITE FOR RESIDUE DMS B 202

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:47 -C:151

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K7I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K7I)

(-) Exons   (0, 0)

(no "Exon" information available for 4K7I)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee......eeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh...hhhhhhhhh......eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k7i A   0 SAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  


Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee......eeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh......hhhhhh......eeeeee..eeeeeee..........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k7i B   1 APIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 


Chain C from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....eeehhhhh...eeeeee........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh......hhhhhh......eeeeee..eeeeeee.............hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k7i C   1 APIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPGTGLTCSLAPNIISQL 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   ||  151       161
                                                                                                                                                                         144|               
                                                                                                                                                                          146
   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 4K7I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K7I)

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)

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  1.11.1.15
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX5_HUMAN | P30044: 1h4o 1hd2 1oc3 1urm 2vl2 2vl3 2vl9 3mng 4k7n 4k7o 4mmm

(-) Related Entries Specified in the PDB File

4k7n 4k7o 4mmm