Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  HUMAN PDRX5 COMPLEX WITH A LIGAND BP7
 
Authors :  J. F. Guichou
Date :  09 Sep 13  (Deposition) - 30 Jul 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A,C,E,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  G  (1x)
Biol. Unit 5:  A,E  (1x)
Biol. Unit 6:  C,G  (1x)
Keywords :  Enzyme, 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, C, E, G
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  1234
Asymmetric Unit : ACEG
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  C  
Biological Unit 3 (1x):   E 
Biological Unit 4 (1x):    G
Biological Unit 5 (1x): A E 
Biological Unit 6 (1x):  C G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BP72Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BP71Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BP71Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1BP7-1Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1BP7-1Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1BP71Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1BP71Ligand/Ion1,1'-BIPHENYL-3,4-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:44 , GLY A:46 , CYS A:47 , ILE A:119 , PHE A:120 , ARG A:127 , HOH A:347 , HOH A:463 , PHE E:79BINDING SITE FOR RESIDUE BP7 A 201
2AC2SOFTWAREPRO A:144 , THR C:44 , GLY C:46 , CYS C:47 , PHE C:120 , ARG C:127 , HOH C:426 , HOH C:437 , PRO G:19 , PHE G:79BINDING SITE FOR RESIDUE BP7 C 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MMM)

(-) 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.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh...hhhhhhhhh......eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmm A   0 SAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  


Chain C from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee......eeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh......hhhhhh......eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmm C   0 SAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  


Chain E from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               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..........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmm E   0 SAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  


Chain G from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               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..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmm G   0 SAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4MMM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BP7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4mmm)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4mmm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRDX5_HUMAN | P30044
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.15
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PRDX5_HUMAN | P30044
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4k7i 4k7n 4k7o

(-) Related Entries Specified in the PDB File

4k7i 4k7n 4k7o