Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE RNR2 HOMODIMER FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. Sommerhalter, W. C. Voegtli, D. L. Perlstein, J. Ge, J. Stubbe, A. C. Rosenzweig
Date :  09 Mar 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sommerhalter, W. C. Voegtli, D. L. Perlstein, J. Ge, J. Stubbe, A. C. Rosenzweig
Structures Of The Yeast Ribonucleotide Reductase Rnr2 And Rnr4 Homodimers.
Biochemistry V. 43 7736 2004
PubMed-ID: 15196016  |  Reference-DOI: 10.1021/BI049510M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN 1
    ChainsA, B, C, D
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRNR2, YJL026W, J1271
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SMQ)

(-) Sites  (0, 0)

(no "Site" information available for 1SMQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SMQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SMQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SMQ)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2_YEAST175-191
 
 
 
  4A:175-191
B:175-191
C:175-191
D:175-191
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2_YEAST175-191
 
 
 
  2A:175-191
-
-
D:175-191
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2_YEAST175-191
 
 
 
  2-
B:175-191
C:175-191
-

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL026W1YJL026W.1X:392398-3935971200RIR2_YEAST1-3993994A:26-359 (gaps)
B:26-359 (gaps)
C:26-359 (gaps)
D:26-359 (gaps)
334
334
334
334

(-) 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:329
 aligned with RIR2_YEAST | P09938 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
           RIR2_YEAST    26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
               SCOP domains d1smqa_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1smqA00 A:26-359 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..-----hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:26-359 (gaps) UniProt: 1-399 [INCOMPLETE]                                                                                                                                                                                                                                                                                     Transcript 1
                 1smq A  26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAAS-----ENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
                                    35        45        55        65        75        85        95       105       115       125       135        |-    |  155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
                                                                                                                                                144   150                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with RIR2_YEAST | P09938 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
           RIR2_YEAST    26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
               SCOP domains d1smqb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1smqB00 B:26-359 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..-----hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:26-359 (gaps) UniProt: 1-399 [INCOMPLETE]                                                                                                                                                                                                                                                                                     Transcript 1
                 1smq B  26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAAS-----ENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
                                    35        45        55        65        75        85        95       105       115       125       135        |-    |  155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
                                                                                                                                                144   150                                                                                                                                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:318
 aligned with RIR2_YEAST | P09938 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
           RIR2_YEAST    26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
               SCOP domains d1smqc_ C: Ribonucleotide reduct           ase R2                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1smqC00 C:26-359 Ribonucleotide            Reductase, subunit A                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------..hhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..-----hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: C:26-359 (gaps) UniProt: 1-399 [INCOMPLETE]                                                                                                                                                                                                                                                                                     Transcript 1
                 1smq C  26 LNKELETLREENRVKSDMLKEKLSKDAENHKA-----------LKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAAS-----ENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
                                    35        45        55 |       -   |    75        85        95       105       115       125       135        |-    |  155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
                                                          57          69                                                                        144   150                                                                                                                                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:318
 aligned with RIR2_YEAST | P09938 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
           RIR2_YEAST    26 LNKELETLREENRVKSDMLKEKLSKDAENHKAYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
               SCOP domains d1smqd_ D: Ribonucleotide reduct           ase R2                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1smqD00 D:26-359 Ribonucleotide            Reductase, subunit A                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) --------------------------------           -------Ribonuc_red_sm-1smqD01 D:76-358                                                                                                                                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) --------------------------------           -------Ribonuc_red_sm-1smqD02 D:76-358                                                                                                                                                                                                                                                            - Pfam domains (2)
           Pfam domains (3) --------------------------------           -------Ribonuc_red_sm-1smqD03 D:76-358                                                                                                                                                                                                                                                            - Pfam domains (3)
           Pfam domains (4) --------------------------------           -------Ribonuc_red_sm-1smqD04 D:76-358                                                                                                                                                                                                                                                            - Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------..hhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..-----hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: D:26-359 (gaps) UniProt: 1-399 [INCOMPLETE]                                                                                                                                                                                                                                                                                     Transcript 1
                 1smq D  26 LNKELETLREENRVKSDMLKEKLSKDAENHKA-----------LKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFISRVLAFFAAS-----ENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
                                    35        45        55 |       -   |    75        85        95       105       115       125       135        |-    |  155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    
                                                          57          69                                                                        144   150                                                                                                                                                                                                                 

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RIR2_YEAST | P09938)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004748    ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor    Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0009186    deoxyribonucleoside diphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005971    ribonucleoside-diphosphate reductase complex    An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

 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
(no "Ligands, Modified Residues, Ions" information available for 1smq)
 
  Sites
(no "Sites" information available for 1smq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1smq)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1smq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RIR2_YEAST | P09938
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.17.4.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RIR2_YEAST | P09938
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RIR2_YEAST | P099381jk0 2cvy

(-) Related Entries Specified in the PDB File

1jk0 STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE Y2Y4 (RNR2RNR4) HETERODIMER FROM SACCHAROMYCES CEREVISIAE
1sms STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE RNR4 HOMODIMER FROM SACCHAROMYCES CEREVISIAE