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
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)

(-) Description

Title :  R2-LIKE LIGAND-BINDING OXIDASE WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR (LONG SOAK)
 
Authors :  J. J. Griese, M. Hogbom
Date :  24 Aug 15  (Deposition) - 09 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  R2-Like Ligand-Binding Oxidase, Diiron Cofactor, Ribonucleotide Reductase R2 Subunit Fold, Metalloprotein Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Griese, R. Kositzki, P. Schrapers, R. M. Branca, A. Nordstrom, J. Lehtio, M. Haumann, M. Hogbom
Structural Basis For Oxygen Activation At A Heterodinuclear Manganese/Iron Cofactor.
J. Biol. Chem. V. 290 25254 2015
PubMed-ID: 26324712  |  Reference-DOI: 10.1074/JBC.M115.675223

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT
    Chains: A
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-46 EK/LIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GK2771
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS (STRAIN HTA426)
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
3MN1Ligand/IonMANGANESE (II) ION
2MN31Ligand/IonMANGANESE (III) ION
4PLM1Ligand/IonPALMITIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
3MN-1Ligand/IonMANGANESE (II) ION
2MN32Ligand/IonMANGANESE (III) ION
4PLM2Ligand/IonPALMITIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:69 , GLU A:102 , HIS A:105 , FE A:402 , PLM A:403 , HOH A:501 , HOH A:521binding site for residue MN3 A 401
2AC2SOFTWAREGLU A:102 , GLU A:167 , GLU A:202 , HIS A:205 , MN3 A:401 , PLM A:403 , HOH A:521binding site for residue FE A 402
3AC3SOFTWAREGLY A:64 , PHE A:65 , GLU A:69 , GLU A:102 , PHE A:135 , GLU A:167 , LEU A:170 , THR A:177 , GLU A:202 , MN3 A:401 , FE A:402 , HOH A:501 , HOH A:521binding site for residue PLM A 403
4AC4SOFTWAREHIS A:130 , HOH A:552 , HOH A:561binding site for residue MN A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCS)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcs A   2 VHHDGFQTVKATIDWEHPMFKLYEKAKRNGKWNPADIDFSQDQKDFASLTSEEKISALPLVAGFSAGEEAVTLDILPMAHALARQGRLEDVLFLTTFMHDEAKHVEMFSRWQQAVGIGQMDLSVFHNDHYKRIFYEALPEAMNRLYADDSPEAVIRAATVYNMIVEGTLAESGYYTFRQIYKKAGLFPGLLQGIDYLNMDEGRHIQFGIYTIQRIVNEDERYYELFIRYMDELWPHVIGYVDYLTELGKRQQQLARTYALEIDYDLLRHYVIKQFNLRKKQISRTKR 288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281
   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 5DCS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dcs)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5dcs
    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
  Q5KW80_GEOKA | Q5KW80
    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)
  1.17.4.1
    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
  Q5KW80_GEOKA | Q5KW80
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5KW80_GEOKA | Q5KW80: 4hr0 4hr4 4hr5 4xb9 4xbv 4xbw 5dco 5dcr 5ekb

(-) Related Entries Specified in the PDB File

4hr0 4HR0 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR (SHORT SOAK, PROTEIN PURIFIED IN PARTIALLY METAL-BOUND FORM).
4hr4 4HR4 CONTAINS THE SAME PROTEIN WITH ANAEROBICALLY RECONSTITUTED MN/ FE COFACTOR.
4hr5 4HR5 CONTAINS THE SAME PROTEIN WITHOUT METAL COFACTOR.
4xb9 4XB9 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIIRON COFACTOR (LONG SOAK).
4xbv 4XBV CONTAINS THE SAME PROTEIN WITH ANAEROBICALLY RECONSTITUTED DIIRON COFACTOR.
4xbw 4XBW CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIMANGANESE COFACTOR.
5dco 5DCO CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIIRON COFACTOR (SHORT SOAK).
5dcr 5DCR CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR (SHORT SOAK).