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 :  CRYSTAL STRUCTURE OF A PUTATIVE CYSTEINE DIOXYGNASE FROM RALSTONIA EUTROPHA: AN ALTERNATIVE MODELING OF 2GM6 FROM JCSG TARGET 361076
 
Authors :  S. H. Hartman, C. M. Driggers, P. A. Karplus, Joint Center For Struct Genomics (Jcsg)
Date :  15 Jun 14  (Deposition) - 26 Nov 14  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative "Gln-Type" Cysteine Dioxygenase, Joint Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Driggers, S. J. Hartman, P. A. Karplus
Structures Of Arg- And Gln-Type Bacterial Cysteine Dioxygenase Homologs.
Protein Sci. V. 24 154 2015
PubMed-ID: 25307852  |  Reference-DOI: 10.1002/PRO.2587

(-) Compounds

Molecule 1 - CYSTEINE DIOXYGENASE TYPE I
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: REUT_B5045, YP_299237.1
    Organism Scientific: RALSTONIA EUTROPHA JMP134
    Organism Taxid: 264198
    Strain: JMP 134 / LMG 1197

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2FE1Ligand/IonFE (III) ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
4OXY1Ligand/IonOXYGEN MOLECULE
5SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:94 , HIS A:96 , HIS A:147 , OXY A:302 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE FE A 301
02AC2SOFTWAREPHE A:83 , HIS A:94 , HIS A:96 , TYR A:164 , ARG A:173 , FE A:301 , HOH A:502BINDING SITE FOR RESIDUE OXY A 302
03AC3SOFTWAREARG A:34 , ARG A:37 , ARG A:148 , SO4 A:304 , EDO A:310 , HOH A:550 , HOH A:657BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREPRO A:30 , GLY A:31 , ARG A:34 , SO4 A:303 , HOH A:550 , HOH A:703BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY A:31 , GLU A:32 , ALA A:33 , EDO A:306 , HOH A:508 , HOH A:566BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWARETHR A:142 , EDO A:305 , HOH A:508 , HOH A:528 , HOH A:566BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREASN A:191 , PRO A:192 , TYR A:193 , HOH A:634BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREARG A:77 , TRP A:99 , HOH A:529 , HOH A:549BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWARETYR A:176 , GLU A:178BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREGLU A:32 , ALA A:33 , ARG A:90 , SO4 A:303 , HOH A:550 , HOH A:566 , HOH A:657BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREALA A:44 , ARG A:45 , ALA A:48 , SER A:119 , GLY A:134 , HOH A:556 , HOH A:609 , HOH A:648BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREASP A:117 , GLY A:118 , HOH A:664BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWAREPRO A:54 , ASP A:55 , ALA A:56 , HOH A:577 , HOH A:583BINDING SITE FOR RESIDUE EDO A 313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QMA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QMA)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhh.......eeeeeee......eeeeeee..............eeeeeee..eeeeeeee.....eee....eee....eeee.......eeeee......eeeeeee..hhhhh.eeee.....eeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qma A  11 SLAPLREFITGLSALLDEQPGEARILREGGALLARLVARDDWLPDAFAQPHPEYYQQmLLHCDSAERFSIVSFVWGPGQRTPIHDHTVWGLIGmLRGAEYSQPFVLDGSGRPVLHGEPTRLEPGHVEAVSPTVGDIHRVHNAYDDRVSISIHVYGANIGGVRRSVYTEAGERKPFISGYSNPYLPNPWDRSK 202
                                    20        30        40        50        60       |70        80        90       100   |   110       120       130       140       150       160       170       180       190       200  
                                                                                    68-MSE                             104-MSE
   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 ; only for superseded entry 2GM6: 1,1)

(no "SCOP Domain" information available for 4QMA, only for superseded entry 2GM6 replaced by 4QMA)

(-) CATH Domains  (0, 0 ; only for superseded entry 2GM6: 2,2)

(no "CATH Domain" information available for 4QMA, only for superseded entry 2GM6 replaced by 4QMA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qma)
 

(-) 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
  4qma
    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
  Q46R41_CUPNJ | Q46R41
    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
  Q46R41_CUPNJ | Q46R41
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4QMA)

(-) Related Entries Specified in the PDB File

2gm6 MODEL WAS REFINED AGAINST DATA FROM THIS ENTRY
3uss ANOTHER "GLN-TYPE" PUTATIVE CYSTEINE DIOXYGENASE
4qm9
4qma