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 :  CRYSTAL STRUCTURES OF THIOREDOXIN WITH MESNA AT 2.8A RESOLUTION
 
Authors :  V. Sridhar, B. Chie-Leon, J. Badger, V. L. Nienaber, F. H. Hausheer
Date :  26 Feb 14  (Deposition) - 29 Oct 14  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6:  A,B,C,D  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Parker, V. L. Nienaber, P. N. Petluru, V. Sridhar, B. D. Leverett, P. Y. Ayala, M. Zhao, B. Chie-Leon, K. Jair, H. Kochat, J. Badger, F. H. Hausheer
Bnp7787 Forms Novel Covalent Adducts On Human Thioredoxin And Modulates Thioredoxin Activity
J Pharmacol Clin Toxicol V. 2 1026 2014
PubMed: search

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TXN, TRDX, TRX, TRX1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRX, ATL-DERIVED FACTOR, ADF, SURFACE-ASSOCIATED SULPHYDRYL PROTEIN, SASP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 6 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1COM4Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1COM2Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1COM2Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1COM-1Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1COM-1Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1COM2Ligand/Ion1-THIOETHANESULFONIC ACID
Biological Unit 6 (1, 4)
No.NameCountTypeFull Name
1COM4Ligand/Ion1-THIOETHANESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:68 , CYS A:69 , PHE A:80 , LYS C:8BINDING SITE FOR RESIDUE COM A 200
2AC2SOFTWAREGLU A:6 , ASP A:61 , CYS A:62 , LYS A:96BINDING SITE FOR RESIDUE COM A 201
3AC3SOFTWAREGLU B:68 , CYS B:69 , GLN B:78 , PHE B:80 , LYS B:85 , LYS D:8BINDING SITE FOR RESIDUE COM B 200
4AC4SOFTWAREGLU B:6 , ASP B:61 , CYS B:62 , LYS B:96BINDING SITE FOR RESIDUE COM B 201

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:32 -A:35
2A:73 -C:62
3B:32 -B:35
4B:73 -D:62
5C:32 -C:69
6C:35 -D:73
7C:73 -D:35
8D:32 -D:69

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:74 -Pro A:75
2Met B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4POL)

(-) 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:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh...ee.eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4pol A   0 TMVKQIESKTAFQKALKAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKKKLEATINKLV 105
                                     9        19        29        39        49        59        69        79        89        99      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh...ee.eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4pol B   0 TMVKQIESKTAFQKALKAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKKKLEATINKLV 105
                                     9        19        29        39        49        59        69        79        89        99      


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhh....eeeee...eee..eeeehhhhhhhhhhh...eeeee.....ee...eeeee...eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4pol C   0 TMVKQIESKTAFQKALKAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKKKLEATINKLV 105
                                     9        19        29        39        49        59        69        79        89        99      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhh....eeeee....ee..eeeehhhhhhhhh....eeeeee.....ee...eeeee...eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4pol D   0 TMVKQIESKTAFQKALKAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKKKLEATINKLV 105
                                     9        19        29        39        49        59        69        79        89        99
   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 4POL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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
    COM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:74 - Pro A:75   [ RasMol ]  
    Met B:74 - Pro B:75   [ RasMol ]  
 
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
  4pol
    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
  THIO_HUMAN | P10599
    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)
  (no 'Enzyme Classificator' available)
    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
  THIO_HUMAN | P10599
    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
        THIO_HUMAN | P10599: 1aiu 1auc 1cqg 1cqh 1ert 1eru 1erv 1erw 1m7t 1mdi 1mdj 1mdk 1trs 1tru 1trv 1trw 1w1c 1w1e 2hsh 2hxk 2ifq 2iiy 3e3e 3kd0 3m9j 3m9k 3qfa 3qfb 3trx 4ll1 4ll4 4oo4 4oo5 4pok 4pom 4puf 4trx 5dqy

(-) Related Entries Specified in the PDB File

4pok 4pom