Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED HPDI (ABB'XA')
 
Authors :  C. Wang, W. Li, J. Ren, H. Ke, W. Gong, W. Feng, C. -C. Wang
Date :  10 Apr 12  (Deposition) - 10 Apr 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A
Keywords :  Abb'A' Domains, "Cghc" Active Sites, Horseshoe Shape, An Enzyme, A Redox-Regulated Chaperone, Endoplasmic Reticulum, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wang, W. Li, J. Ren, J. Fang, H. Ke, W. Gong, W. Feng, C. -C. Wang
Structural Insights Into The Redox-Regulated Dynamic Conformations Of Human Protein Disulfide Isomerase
Antioxid Redox Signal V. 19 44 2013
PubMed-ID: 22657537  |  Reference-DOI: 10.1089/ARS.2012.4630

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE
    Chains: A
    EC Number: 5.3.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET32A
    Expression System Strain: CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: REDUCED FULL-LENGTH HPDI, UNP RESIDUES 18-479
    Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PDI, CELLULAR THYROID HORMONE-BINDING PROTEIN, PROLYL 4- HYDROXYLASE SUBUNIT BETA, P55

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4EKZ)

(-) Sites  (0, 0)

(no "Site" information available for 4EKZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:0 -Asp A:18
2Tyr A:99 -Pro A:100
3Cys A:312 -Pro A:313
4Phe A:440 -Pro A:441

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EKZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee..eee....hhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.......ee.....hhhhhhhhhhhhh....ee..hhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhhh.....eeeeee.....eee.....hhhhhhhhhhhhh...ee..hhhhhh...eeeeee......hhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh........eeeeee....ee.......hhhhhhhhhhhhhh.....................eeehhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...............eeeee........ee.....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ekz A -14 HHSSGLEVLFQGPGSDAPEEEDHVLVLRKSNFAEALAAHKYLLVEFYAPWCGHCKALAPEYAKAAGKLKAEGSEIRLAKVDATEESDLAQQYGVRGYPTIKFFRNGDTASPKEYTAGREADDIVNWLKKRTGPAATTLPDGAAAESLVESSEVAVIGFFKDVESDSAKQFLQAAEAIDDIPFGITSNSDVFSKYQLDKDGVVLFKKFDEGRNNFEGEVTKENLLDFIKHNQLPLVIEAPKIFGGEIKTHILLFLPKSVSDYDGKLSNFKTAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEMTKYKPESEELTAERITEFCHRFLEGKIKPHLMSQELPEDWDKQPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQDGA 478
                                    -5    ||  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      |247       257       267       277       287       297       307       317   ||  329       339       349       359       369       379       389       399       409       419       429       439       449       459       469         
                                          0|                                                                                                                                                                                                                          239|                                                                         321|                                                                                                                                                          
                                          18                                                                                                                                                                                                                           245                                                                          324
   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 4EKZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 4ekz)
 
  Sites
(no "Sites" information available for 4ekz)
 
  Cis Peptide Bonds
    Cys A:312 - Pro A:313   [ RasMol ]  
    Phe A:440 - Pro A:441   [ RasMol ]  
    Ser A:0 - Asp A:18   [ RasMol ]  
    Tyr A:99 - Pro A:100   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  4ekz
    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
  PDIA1_HUMAN | P07237
    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)
  5.3.4.1
    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
  PDIA1_HUMAN | P07237
    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
        PDIA1_HUMAN | P07237: 1bjx 1mek 1x5c 2bjx 2k18 3bj5 3uem 4el1 4ju5

(-) Related Entries Specified in the PDB File

3uem SHORT FORM OF THE SAME PROTEIN
4el1 OXIDIZED FULL-LENGTH HPDI