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(-) Description

Title :  N-TERMINAL DOMAIN OF VDUP-1
 
Authors :  G. Polekhina, S. F. Kok, D. B. Ascher, M. Waltham
Date :  02 Aug 12  (Deposition) - 27 Feb 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Biol. Unit 9:  I  (1x)
Biol. Unit 10:  J  (1x)
Keywords :  Alpha-Arrestin, Oxidative Stress, Metabolism, Thioredoxin, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Polekhina, D. B. Ascher, S. F. Kok, S. Beckham, M. Wilce, M. Waltham
Structure Of The N-Terminal Domain Of Human Thioredoxin-Interacting Protein.
Acta Crystallogr. , Sect. D V. 69 333 2013
PubMed-ID: 23519408  |  Reference-DOI: 10.1107/S0907444912047099

(-) Compounds

Molecule 1 - THIOREDOXIN-INTERACTING PROTEIN
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PMCSG7
    Expression System Strain: EC538
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 2-149
    Gene: TXNIP, VDUP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THIOREDOXIN-BINDING PROTEIN 2, VITAMIN D3 UP-REGULATED PROTEIN 1

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): A         
Biological Unit 2 (1x):  B        
Biological Unit 3 (1x):   C       
Biological Unit 4 (1x):    D      
Biological Unit 5 (1x):     E     
Biological Unit 6 (1x):      F    
Biological Unit 7 (1x):       G   
Biological Unit 8 (1x):        H  
Biological Unit 9 (1x):         I 
Biological Unit 10 (1x):          J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 9 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 10 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:74 , THR A:75 , ASP F:74 , THR F:75BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP C:74 , THR C:75 , ASP J:74 , THR J:75BINDING SITE FOR RESIDUE CA C 201
3AC3SOFTWAREASP B:74 , THR B:75 , ASP D:74 , THR D:75BINDING SITE FOR RESIDUE CA D 201
4AC4SOFTWAREASP E:74 , THR E:75 , ASP H:74 , THR H:75BINDING SITE FOR RESIDUE CA H 201
5AC5SOFTWAREASP I:74 , THR I:75BINDING SITE FOR RESIDUE CA I 201

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:63 -B:63
2C:63 -D:63
3E:63 -F:63
4G:63 -H:63
5I:63 -J:63

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly E:119 -Ser E:120
2Thr G:112 -Ser G:113
3Glu I:79 -Asp I:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEJ)

(-) 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:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej A   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77||      95       105       115       125       135       145    
                                                                                                 78|                                                              
                                                                                                  87                                                              


Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej B   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       113       123       133       143      
                                                                                                   80|                                                              
                                                                                                    87                                                              


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej C   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       113       123       133       143      
                                                                                                   80|                                                              
                                                                                                    87                                                              


Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej D   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       113|      128       138       148 
                                                                                                   80|                       113|                              
                                                                                                    87                        119                              


Chain E from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej E   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDQPTGENEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147  


Chain F from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej F   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       113       123       133       143      
                                                                                                   80|                                                              
                                                                                                    87                                                              


Chain G from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej G   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       113       123       133       143      
                                                                                                   80|                                                              
                                                                                                    87                                                              


Chain H from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej H   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDQPTGENEMVIMRPGNKYEYKFGFELPQGPLGTSFYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77        87        97       107      |120       130       140         
                                                                                                                                    114|                               
                                                                                                                                     118                               


Chain I from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej I   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDQPTGENEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYGSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147  


Chain J from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gej J   8 KSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQGSQQCKQTSEYLRYEDTLLLEDEMVIMRPGNKYEYKFGFELPQGPLGTSVDYWVKAFLDRPSQPTQETKKNFEVVDLV 149
                                    17        27        37        47        57        67        77  ||    93       103       120       130       140         
                                                                                                   80|                      112|                             
                                                                                                    87                       120
   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 4GEJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

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 Related Entries

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

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        TXNIP_HUMAN | Q9H3M7: 4gei 4gfx 4ll1 4ll4 4rof 4roj 5cq2 5df6 5dws 5dzd

(-) Related Entries Specified in the PDB File

4gei