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(-) Description

Title :  CRYSTAL STRUCTURE OF TT0972 PROTEIN FORM THERMUS THERMOPHILUS WITH CL(-) IONS
 
Authors :  E. Inagaki, N. Nakano, A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Feb 06  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Dodecamer, Flavin, Chloride Ion, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Inagaki, N. Nakano, A. Shinkai, S. Yokoyama
Crystal Structure Of Tt0972 Protein Form Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TT0972 PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , GLU B:19 , GLU C:19 , GLU D:68BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWARELYS A:6 , LYS D:6 , LYS F:6BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWARELYS B:6 , LYS C:6 , LYS E:6BINDING SITE FOR RESIDUE CL B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DEH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DEH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DEH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DEH)

(-) Exons   (0, 0)

(no "Exon" information available for 2DEH)

(-) 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:68
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2deha_ A: automated matches                                         SCOP domains
               CATH domains 2dehA00 A:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2deh A  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61        


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2dehb_ B: automated matches                                         SCOP domains
               CATH domains 2dehB00 B:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2deh B  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61        


Chain C from PDB  Type:PROTEIN  Length:67
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2dehc_ C: automated matches                                        SCOP domains
               CATH domains 2dehC00 C:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2deh C  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
                                    11        21        31        41        51        61       


Chain D from PDB  Type:PROTEIN  Length:67
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2dehd_ D: automated matches                                        SCOP domains
               CATH domains 2dehD00 D:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2deh D  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
                                    11        21        31        41        51        61       


Chain E from PDB  Type:PROTEIN  Length:67
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2dehe_ E: automated matches                                        SCOP domains
               CATH domains 2dehE00 E:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2deh E  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
                                    11        21        31        41        51        61       


Chain F from PDB  Type:PROTEIN  Length:67
 aligned with Q72IR6_THET2 | Q72IR6 from UniProtKB/TrEMBL  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
          Q72IR6_THET2    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2dehf_ F: automated matches                                        SCOP domains
               CATH domains 2dehF00 F:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2deh F  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
                                    11        21        31        41        51        61
   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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DEH)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2DEH)

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 Related Entries

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        Q72IR6_THET2 | Q72IR6: 2dev

(-) Related Entries Specified in the PDB File

2cz8 THE SAME PROTEIN COMPLEXED WITH PHOSPHATE IONS, POTASSIUM IONS AND FLAVIN COMPAUNDS.
2deg TT0972 PROTEIN FORM THERMUS THERMOPHILUS WITH MN2(+) IONS RELATED ID: TTK003000972.3 RELATED DB: TARGETDB