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 THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH MES IN THE ACTIVE SITE
 
Authors :  O. Aurelius, R. Johansson, V. Bagenholm, T. Beck, A. Balhuizen, D. Lund B. M. Sjoberg, E. Mulliez, D. T. Logan
Date :  29 Jan 14  (Deposition) - 14 Jan 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Radical Chemistry, Allosteric Regulation, Anaerobic Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Aurelius, R. Johansson, V. Bagenholm, T. Beck, A. Balhuizen, D. Lundin, B. M. Sjoberg, E. Mulliez, D. T. Logan
The Crystal Structure Of Thermotoga Maritima Class Iii Ribonucleotide Reductase Lacks A Radical Cysteine Pre- Positioned In The Active Site.
Plos One V. 10 01281 2015
PubMed-ID: 26147435  |  Reference-DOI: 10.1371/JOURNAL.PONE.0128199

(-) Compounds

Molecule 1 - ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIL
    Expression System Vector: PRSFDUET-1
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: ANAEROBIC RIBONUCLEOTIDE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:594 , HIS A:598 , CYS A:605 , CYS A:608BINDING SITE FOR RESIDUE ZN A 700
2AC2SOFTWARECYS B:594 , HIS B:598 , CYS B:605 , CYS B:608BINDING SITE FOR RESIDUE ZN B 652
3AC3SOFTWAREHIS A:114 , TYR A:124 , TYR A:227 , PRO A:498 , ALA A:499 , GLU A:500 , HOH A:2068 , HOH A:2329BINDING SITE FOR RESIDUE MES A1634
4AC4SOFTWAREHIS B:114 , TYR B:124 , TYR B:227 , VAL B:497 , PRO B:498 , ALA B:499 , GLU B:500 , HOH B:2066 , HOH B:2075 , HOH B:2107 , HOH B:2275 , HOH B:2278BINDING SITE FOR RESIDUE MES B1631
5AC5SOFTWAREARG B:221 , HOH B:2128 , HOH B:2328BINDING SITE FOR RESIDUE 1PE B1632

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:282 -Pro A:283
2Phe B:282 -Pro B:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4COM)

(-) 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:601
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhh......ee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..ee.hhhhhhhhhhhhh....eeeeee..hhhhhh...................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh...eeee...eee.....ee.............eeeee....eeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4com A   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRRGVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLGESFKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKER 633
                                    10        20        30        40        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      |352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632 
                                                                           49|                                                                                                                                                                                                                                                                        330|                                                                                                                                                                                                                                                                                           
                                                                            63                                                                                                                                                                                                                                                                         350                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:596
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhh......ee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..ee.hhhhhhhhhhhhh....eeeeee.........................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eeeee..eee.....ee.............eeeee....eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4com B   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRRRVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLGESFKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFN 630
                                    10        20        30        40       |63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    || 354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624      
                                                                          48|                                                                                                                                                                                                                                                                       328|                                                                                                                                                                                                                                                                                        
                                                                           62                                                                                                                                                                                                                                                                        350
   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 4COM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
    Phe A:282 - Pro A:283   [ RasMol ]  
    Phe B:282 - Pro B:283   [ 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
  4com
    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
  Q9WYL6_THEMA | Q9WYL6
    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)
  1.17.4.2
    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
  Q9WYL6_THEMA | Q9WYL6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9WYL6_THEMA | Q9WYL6: 4coi 4coj 4col 4con 4u3e

(-) Related Entries Specified in the PDB File

4coi CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH GLYCEROL IN THE ACTIVE SITE
4coj CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH DATP AND CTP
4col CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH DATP BOUND IN THE SPECIFICITY SITE
4con CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH CITRATE IN THE ACTIVE SITE