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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF AIBR IN COMPLEX WITH ISOVALERYL COENZYME A AND OPERATOR DNA
 
Authors :  T. Bock, C. Volz, R. Mueller, W. Blankenfeldt
Date :  27 May 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C (1x),D (1x),E (1x),F (1x)
Keywords :  Tetr Like Regulator, Isovaleryl Coenzyme A, Regulation, Operator Dna, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Bock, C. Volz, R. Mueller, W. Blankenfeldt
Crystal Structure Of Aibr In Complex With Isovaleryl Coenzyme A And Operator Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Gene: MXAN_4263
    Organism Scientific: MYXOCOCCUS XANTHUS DK 1622
    Organism Taxid: 246197
 
Molecule 2 - DNA (32-MER)
    Chains: E, F
    Engineered: YES
    Organism Scientific: MYXOCOCCUS XANTHUS DK 1622
    Organism Taxid: 246197
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  EF
Biological Unit 2 (1x):   C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1IVC4Ligand/IonISOVALERYL-COENZYME A
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1IVC2Ligand/IonISOVALERYL-COENZYME A
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1IVC2Ligand/IonISOVALERYL-COENZYME A

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:169 , LYS A:172 , TRP A:173 , PHE A:174 , LYS A:175 , GLY A:178 , ARG A:179 , LEU A:180 , HOH A:401 , HOH A:407 , MET B:69 , PHE B:72 , VAL B:109 , ASP B:128 , LYS B:131 , LYS B:132 , THR B:157 , PHE B:161 , HOH B:401binding site for residue IVC A 301
2AC2SOFTWAREMET A:69 , PHE A:72 , VAL A:109 , ASP A:128 , LYS A:131 , LYS A:132 , VAL A:135 , THR A:157 , PHE A:161 , LEU A:164 , LEU A:168 , TRP B:169 , LYS B:172 , TRP B:173 , PHE B:174 , LYS B:175 , GLY B:178 , ARG B:179 , LEU B:180 , HOH B:405binding site for residue IVC B 301
3AC3SOFTWARETRP C:169 , LYS C:172 , TRP C:173 , LYS C:175 , GLY C:178 , ARG C:179 , LEU C:180 , HOH C:404 , HOH C:405 , ASP D:128 , LYS D:131 , LYS D:132 , PHE D:161 , LEU D:164 , LEU D:168binding site for residue IVC C 301
4AC4SOFTWAREVAL C:109 , ASP C:128 , LYS C:131 , LYS C:132 , TYR C:134 , VAL C:135 , PHE C:161 , LEU C:168 , HOH C:402 , TRP D:169 , LYS D:172 , TRP D:173 , PHE D:174 , LYS D:175 , GLY D:178 , ARG D:179 , LEU D:180 , HOH D:403 , HOH D:405binding site for residue IVC D 301
5AC5SOFTWARETHR A:34 , SER A:35 , MET A:36 , THR A:46 , LYS A:47 , ALA A:48 , TYR A:51 , LYS A:57 , SER B:35 , SER C:35 , ALA C:48 , THR D:34 , SER D:35 , MET D:36 , LYS D:47 , ALA D:48 , TYR D:51 , LYS D:57 , DC E:2 , DT E:3 , DA E:4 , DC E:6 , DA E:8 , DT E:9 , DC E:10 , DG E:11 , DG E:12 , DT E:13 , DG E:15 , DC F:2 , DT F:3 , DA F:4 , DC F:6 , DA F:8 , DT F:9 , DC F:10 , DG F:11 , DG F:12 , DT F:13 , DG F:15 , HOH F:101 , HOH F:106binding site for Di-nucleotide DG E 7 and DA F 14
6AC6SOFTWARETHR A:34 , SER A:35 , MET A:36 , THR A:46 , LYS A:47 , ALA A:48 , TYR A:51 , LYS A:57 , SER B:35 , SER C:35 , ALA C:48 , THR D:34 , SER D:35 , MET D:36 , LYS D:47 , ALA D:48 , TYR D:51 , LYS D:57 , DC E:2 , DT E:3 , DA E:4 , DC E:6 , DA E:8 , DT E:9 , DC E:10 , DG E:11 , DG E:12 , DT E:13 , DG E:15 , DC F:2 , DT F:3 , DA F:4 , DC F:6 , DA F:8 , DT F:9 , DC F:10 , DG F:11 , DG F:12 , DT F:13 , DG F:15 , HOH F:101 , HOH F:106binding site for Di-nucleotide DG F 7 and DA E 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K7Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K7Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K7Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K7Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5K7Z)

(-) 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k7z A  13 ERYRAILETAARLICDRGYEGTSMQEIAAACRMTKAGLYHHIQNKEQLLFAIMNYGMDLFEEQVLSRVQDIANPVERLRACMRHNILLVTRGWSKEVIIILHEHATLTGETRAFIDARKKKYVDFLEEAFSQASQQGLIRPVDPTVGAFSFLGMVLWIYKWFKPDGRLTDEQIADGMVGMLFPPF 197
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k7z B  14 RYRAILETAARLICDRGYEGTSMQEIAAACRMTKAGLYHHIQNKEQLLFAIMNYGMDLFEEQVLSRVQDIANPVERLRACMRHNILLVTRGWSKEVIIILHEHATLTGETRAFIDARKKKYVDFLEEAFSQASQQGLIRPVDPTVGAFSFLGMVLWIYKWFKPDGRLTDEQIADGMVGMLFPPF 197
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    


Chain C from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k7z C  13 ERYRAILETAARLICDRGYEGTSMQEIAAACRMTKAGLYHHIQNKEQLLFAIMNYGMDLFEEQVLSRVQDIANPVERLRACMRHNILLVTRGWSKEVIIILHEHATLTGETRAFIDARKKKYVDFLEEAFSQASQQGLIRPVDPTVGAFSFLGMVLWIYKWFKPDGRLTDEQIADGMVGMLFPPF 197
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     


Chain D from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k7z D  14 RYRAILETAARLICDRGYEGTSMQEIAAACRMTKAGLYHHIQNKEQLLFAIMNYGMDLFEEQVLSRVQDIANPVERLRACMRHNILLVTRGWSKEVIIILHEHATLTGETRAFIDARKKKYVDFLEEAFSQASQQGLIRPVDPTVGAFSFLGMVLWIYKWFKPDGRLTDEQIADGMVGMLFPPF 197
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    


Chain E from PDB  Type:DNA  Length:16
                                                
                 5k7z E   1 CCTACCGATCGGTAGG  16
                                    10      


Chain F from PDB  Type:DNA  Length:16
                                                
                 5k7z F   1 CCTACCGATCGGTAGG  16
                                    10
   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 5K7Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K7Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K7Z)

(-) Gene Ontology  (3, 3)

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
    IVC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5k7z)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  5k7z
    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
  Q1D4I5_MYXXD | Q1D4I5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q1D4I5_MYXXD | Q1D4I5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q1D4I5_MYXXD | Q1D4I5: 5k7f 5k7h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5K7Z)