Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CYSTEINE DIOXYGENASE VARIANT - C93A AT PH 8.0 WITH CYSTEINE
 
Authors :  C. M. Driggers, P. A. Karplus
Date :  25 Dec 14  (Deposition) - 16 Mar 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Cupin Fold, Cysteine To Cysteine Sulfinic Acid Catalysis, Cytosol, Thiol Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Driggers, K. M. Kean, L. L. Hirschberger, R. B. Cooley, M. H. Stipanuk, P. A. Karplus
Structure-Based Insights Into The Role Of The Cys-Tyr Crosslink And Inhibitor Recognition By Mammalian Cysteine Dioxygenase.
J. Mol. Biol. V. 428 3999 2016
PubMed-ID: 27477048  |  Reference-DOI: 10.1016/J.JMB.2016.07.012

(-) Compounds

Molecule 1 - CYSTEINE DIOXYGENASE TYPE 1
    Chains: A
    EC Number: 1.13.11.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDO1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: CYSTEINE DIOXYGENASE TYPE I,CDO-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CYS1Mod. Amino AcidCYSTEINE
3FE1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:140 , CYS A:502 , CL A:503binding site for residue FE A 501
2AC2SOFTWARETYR A:58 , ARG A:60 , LEU A:75 , HIS A:86 , HIS A:88 , HIS A:140 , HIS A:155 , TYR A:157 , MET A:179 , FE A:501 , CL A:503 , HOH A:773 , HOH A:774binding site for residue CYS A 502
3AC3SOFTWAREHIS A:88 , HIS A:140 , HIS A:155 , TYR A:157 , FE A:501 , CYS A:502 , HOH A:745binding site for residue CL A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XF0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XF0)

(-) Exons   (0, 0)

(no "Exon" information available for 4XF0)

(-) Sequences/Alignments

Asymmetric/Biological 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhh.......eeeeee......eeeeeee.......ee.....eeeeeeee..eeeeee.............eeeee....eeee.....eeeee.......eeeeeeee....eeeee......eeeee....ee..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xf0 A   5 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHAFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPC 502
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184     ||
                                                                                                                                                                                                                   190|
                                                                                                                                                                                                                    502
   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 4XF0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XF0)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CYS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:158 - Pro A:159   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4xf0
    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
  CDO1_RAT | P21816
    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)
  1.13.11.20
    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
  CDO1_RAT | P21816
    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
        CDO1_RAT | P21816: 2b5h 2gh2 3eln 4ieo 4iep 4ieq 4ier 4ies 4iet 4ieu 4iev 4iew 4iex 4iey 4iez 4jtn 4jto 4kwj 4kwk 4kwl 4pix 4piy 4piz 4pjy 4ubg 4ubh 4xet 4xez 4xf1 4xf3 4xf4 4xf9 4xfa 4xfb 4xfc 4xff 4xfg 4xfh 4xfi 4yni 4ysf 4yyo 4z82 5efu 5ezw 5fdb 5i0r 5i0s 5i0t 5i0u

(-) Related Entries Specified in the PDB File

4ext FE-CL BOUND Y157F AT PH ~7.0 IN THE PRESENCE OF AZIDE
4ieo UNLIGANDED WT CDO AT PH 4.0 IN THE PRESENCE OF CYS
4iep UNLIGANDED WT CDO AT PH 4.5 IN THE PRESENCE OF CYS
4ieq UNLIGANDED WT CDO AT PH 5.0 IN THE PRESENCE OF CYS
4ier CYS-PERSULFENATE BOUND WT CDO AT PH 5.5 IN THE PRESENCE OF CYS
4ies CYS-PERSULFEANTE BOUND WT CDO AT PH 6.2 IN THE PRESENCE OF CYS
4iet CYS-PERSULFEANTE BOUND WT CDO AT PH 6.8 IN THE PRESENCE OF CYS
4ieu CYS-PERSULFENATE BOUND WT CDO AT PH 7.0 IN THE PRESENCE OF CYS
4iev CYS-ONLY BOUND WT CDO AT PH 8.0 IN THE PRESENCE OF CYS
4iew CYS-ONLY BOUND CYSTEINE DIOXYGENASE AT PH 9.0 IN THE PRESENCE OF CYS
4iex UNLIGANDED ROOM-TEMP WT CDO AT PH 6.2
4iey CYS-PERSULFEANTE BOUND WT CDO AT PH 7.0 IN THE PRESENCE OF CYS,HOME- SOURCE STRUCTURE
4iez UNLIGANDED WT CDO AT PH 8.0
4jtn WT CDO AT PH 8.0 IN THE PRESENCE OF DITHIONITE
4jto CYS-ONLY BOUND WT CDO AT PH 8.0 IN THE PRESENCE OF CYS AND DITHIONITE
4kwk CYS-PERSULFIDE BOUND WT CDO
4kwl 3-MERCAPTOPROPIONATE-PERSULFIDE BOUND WT CDO
4pix UNLIGANDED C93A CDO AT PH 6.2
4piy HOMOCYSTEINE-BOUND C93A CDO AT PH 6.2
4piz HOMOCYSTEINE-BOUND WT CDO AT PH 6.2
4pjy AZIDE-BOUND WT CDO AT PH 6.2
4xez CYSTEINE DIOXYGENASE VARIANT - Y157F AT PH 8.0 WITH DITHIONITE