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 DIMERIC CHLORITE DISMUTASE FROM CYANOTHECE SP. PCC7425 IN COMPLEX WITH ISOTHIOCYANATE
 
Authors :  D. Puehringer, I. Schaffner, G. Mlynek, C. Obinger, K. Djinovic-Carug
Date :  31 May 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Chlorite Dismutase, Cyanobacteria, Heme, Ferredoxin-Like Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Schaffner, G. Mlynek, N. Flego, D. Puehringer, J. Libiseller-Egger, L. Coates, S. Hofbauer, M. Bellei, P. G. Furtmueller, G. Battistuzzi, G. Smulevich, K. Djinovic-Carugo C. Obinger
Crystal Structure Of Dimeric Chlorite Dismutase From Cyanothece Sp. Pcc7425 In Complex With Isothiocyanate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHLORITE DISMUTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Gene: CYAN7425_1434
    Organism Scientific: CYANOTHECE SP. (STRAIN PCC 7425 / ATCC 29141)
    Organism Taxid: 395961
    Strain: PCC 7425 / ATCC 29141

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x):  BCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IS84Ligand/IonISOTHIOCYANATE
4MG1Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 19)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IS84Ligand/IonISOTHIOCYANATE
4MG-1Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 15)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IS83Ligand/IonISOTHIOCYANATE
4MG-1Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:128 , LEU A:129 , PHE A:145 , HEM A:502binding site for residue IS8 A 501
02AC2SOFTWAREILE A:59 , ARG A:60 , TYR A:61 , ALA A:62 , LEU A:70 , ILE A:90 , LYS A:92 , TRP A:96 , PHE A:108 , HIS A:114 , THR A:115 , GLY A:118 , VAL A:125 , ARG A:127 , PHE A:141 , PHE A:145 , LEU A:158 , LEU A:159 , MET A:162 , TRP A:168 , IS8 A:501 , HOH A:623 , HOH A:638 , HOH A:639 , HOH A:679binding site for residue HEM A 502
03AC3SOFTWAREILE A:36 , ARG A:128 , TRP A:144 , HOH A:607 , HOH A:643 , HOH A:707binding site for residue GOL A 503
04AC4SOFTWAREARG A:4 , HOH A:669 , ARG B:4binding site for residue SO4 A 504
05AC5SOFTWAREILE B:59 , ARG B:60 , TYR B:61 , ALA B:62 , LEU B:70 , ILE B:90 , LYS B:92 , PHE B:108 , HIS B:114 , THR B:115 , GLY B:118 , ARG B:127 , PHE B:141 , PHE B:145 , LEU B:158 , MET B:162 , TRP B:168 , IS8 B:202 , HOH B:330 , HOH B:370 , HOH B:390 , HOH B:399binding site for residue HEM B 201
06AC6SOFTWAREARG B:128 , LEU B:129 , PHE B:145 , HEM B:201 , HOH B:361binding site for residue IS8 B 202
07AC7SOFTWAREILE B:36 , ARG B:128 , TRP B:144 , HOH B:345 , HOH B:392binding site for residue GOL B 203
08AC8SOFTWAREARG A:133 , ALA B:56 , SER B:57 , ASN B:58 , HOH B:304binding site for residue GOL B 204
09AC9SOFTWAREALA A:56 , SER A:57 , ASN A:58 , TRP B:97 , ARG B:133 , HOH B:320binding site for residue GOL B 205
10AD1SOFTWAREARG C:128 , LEU C:129 , PHE C:145 , HEM C:502binding site for residue IS8 C 501
11AD2SOFTWAREILE C:59 , ARG C:60 , TYR C:61 , ALA C:62 , LEU C:70 , ILE C:90 , LYS C:92 , PHE C:108 , HIS C:114 , THR C:115 , GLY C:118 , ARG C:127 , PHE C:141 , PHE C:145 , LEU C:158 , MET C:162 , TRP C:168 , IS8 C:501 , HOH C:618 , HOH C:635 , HOH C:646 , HOH C:716binding site for residue HEM C 502
12AD3SOFTWAREALA C:56 , SER C:57 , ASN C:58 , HOH C:611 , HOH C:630 , TRP D:97 , ARG D:133binding site for residue GOL C 503
13AD4SOFTWAREGLY C:136 , GLU C:137 , GLU C:138binding site for residue GOL C 504
14AD5SOFTWAREARG C:133 , HOH C:727 , ALA D:56 , SER D:57 , ASN D:58 , HOH D:374binding site for residue GOL C 505
15AD6SOFTWARETRP C:15 , ILE C:36 , ARG C:128 , TRP C:144 , HOH C:602 , HOH C:746binding site for residue GOL C 506
16AD7SOFTWAREARG C:4 , HOH C:603 , ARG D:4binding site for residue SO4 C 507
17AD8SOFTWAREHOH B:333 , HOH B:405 , HOH B:513 , HOH C:745binding site for residue MG C 508
18AD9SOFTWAREILE D:59 , ARG D:60 , TYR D:61 , ALA D:62 , LEU D:70 , ILE D:90 , LYS D:92 , TRP D:96 , PHE D:108 , HIS D:114 , THR D:115 , GLY D:118 , ARG D:127 , PHE D:141 , THR D:143 , PHE D:145 , LEU D:158 , LEU D:159 , MET D:162 , TRP D:168 , IS8 D:202 , HOH D:312 , HOH D:319 , HOH D:360 , HOH D:362binding site for residue HEM D 201
19AE1SOFTWAREARG D:128 , LEU D:129 , PHE D:145 , HEM D:201binding site for residue IS8 D 202
20AE2SOFTWAREARG D:128 , TRP D:144 , HOH D:308 , HOH D:331binding site for residue GOL D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K90)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:122 -Pro A:123
2Leu B:122 -Pro B:123
3Leu C:122 -Pro C:123
4Leu D:122 -Pro D:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K90)

(-) Exons   (0, 0)

(no "Exon" information available for 5K90)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeeeeee........eeeeee....eeeeee.......hhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee.hhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k90 A   2 NNRYSFIGGRTGQWQVVKIRNVLGPGLQLVEKVNILNGASAWRLQGFASNIRYAIRTELEALQAVQPMLNRAEAILAVLIPIKKSAQWWEMAQDERRDIFERESHHTAVGLEYLPGVARRLLHCRDLGEEFDFLTWFEFAPEHSSAFNELLLRMRASKEWEYVEREVEVWLKRL 182
                                    11        21        31        48        58        68        78        88        98       108       118       128       138       148       158       168       178    
                                                                 40|                                                                                                                                      
                                                                  48                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeeeeee........eeeeee.....eeeeee.......hhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee.hhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k90 B   2 NNRYSFIGGRTGQWQVVKIRNVLGPGLQLVEKVNILNGADSAWRLQGFASNIRYAIRTELEALQAVQPMLNRAEAILAVLIPIKKSAQWWEMAQDERRDIFERESHHTAVGLEYLPGVARRLLHCRDLGEEFDFLTWFEFAPEHSSAFNELLLRMRASKEWEYVEREVEVWLKRL 182
                                    11        21        31        47        57        67        77        87        97       107       117       127       137       147       157       167       177     
                                                                 40|                                                                                                                                       
                                                                  47                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeeeeee........eeeeee....eeeeee.......hhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee.hhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k90 C   2 NNRYSFIGGRTGQWQVVKIRNVLGPGLQLVEKVNILNGDSAWRLQGFASNIRYAIRTELEALQAVQPMLNRAEAILAVLIPIKKSAQWWEMAQDERRDIFERESHHTAVGLEYLPGVARRLLHCRDLGEEFDFLTWFEFAPEHSSAFNELLLRMRASKEWEYVEREVEVWLKRL 182
                                    11        21        31       |48        58        68        78        88        98       108       118       128       138       148       158       168       178    
                                                                39|                                                                                                                                       
                                                                 47                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeeeeee........eeeeee.....eeeeee.......hhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee.hhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k90 D   2 NNRYSFIGGRTGQWQVVKIRNVLGPGLQLVEKVNILNGADSAWRLQGFASNIRYAIRTELEALQAVQPMLNRAEAILAVLIPIKKSAQWWEMAQDERRDIFERESHHTAVGLEYLPGVARRLLHCRDLGEEFDFLTWFEFAPEHSSAFNELLLRMRASKEWEYVEREVEVWLKRL 182
                                    11        21        31        47        57        67        77        87        97       107       117       127       137       147       157       167       177     
                                                                 40|                                                                                                                                       
                                                                  47
   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 5K90)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K90)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K90)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5K90)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IS8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
    AE2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:122 - Pro A:123   [ RasMol ]  
    Leu B:122 - Pro B:123   [ RasMol ]  
    Leu C:122 - Pro C:123   [ RasMol ]  
    Leu D:122 - Pro D:123   [ RasMol ]  
 
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
  5k90
    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
  B8HNS6_CYAP4 | B8HNS6
    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
  B8HNS6_CYAP4 | B8HNS6
    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
        B8HNS6_CYAP4 | B8HNS6: 5k8z 5k91

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5K90)