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(-) Description

Title :  CRYSTAL STRUCTURE OF A RIBONUCLEOTIDE REDUCTASE M2 B (RNRR2) FROM HOMO SAPIENS AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Tcell)
Date :  02 Feb 12  (Deposition) - 09 May 12  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Replication, P53 Inducible, Metal-Binding, Nucleus, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg), Partnership For T-Cell Biology (Tcell)
Crystal Structure Of A Ribonucleotide Reductase M2 B (Rnrr2 From Homo Sapiens At 2. 20 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B
    ChainsA, B
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainPB1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRRM2B, P53R2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTP53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE M2 B, P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2-LIKE PROTEIN, P53R2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:145 , ILE B:146 , ARG B:147 , ASP B:148 , LYS B:151BINDING SITE FOR RESIDUE SO4 B 400
2AC2SOFTWARELYS B:28 , THR B:182 , PHE B:183 , ARG B:186BINDING SITE FOR RESIDUE EDO B 401
3AC3SOFTWAREHOH A:427 , HIS B:91 , MSE B:162 , ALA B:269 , HOH B:514BINDING SITE FOR RESIDUE EDO B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:45 -Pro A:46
2Phe B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 20)

Asymmetric/Biological Unit (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_076280P33SRIR2B_HUMANUnclassified387906892A/BP33S
02UniProtVAR_046217W64RRIR2B_HUMANDisease (MTDPS8A)515726182A/BW64R
03UniProtVAR_065122R110HRIR2B_HUMANDisease (MTDPS8B)267607025A/BR110H
04UniProtVAR_025699V115LRIR2B_HUMANUnclassified  ---A/BV115L
05UniProtVAR_065123R121HRIR2B_HUMANDisease (MTDPS8B)267607024A/BR121H
06UniProtVAR_046219E194GRIR2B_HUMANDisease (MTDPS8A)515726191A/BE194G
07UniProtVAR_046220E194KRIR2B_HUMANDisease (MTDPS8A)121918308A/BE194K
08UniProtVAR_046221I224SRIR2B_HUMANDisease (MTDPS8A)515726196A/BI224S
09UniProtVAR_046222C236FRIR2B_HUMANDisease (MTDPS8A)121918309A/BC236F
10UniProtVAR_046223M282IRIR2B_HUMANDisease (MTDPS8A)182614164A/BM282I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2B_HUMAN130-146
 
  2A:130-146
B:130-146

(-) Exons   (0, 0)

(no "Exon" information available for 4DJN)

(-) 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:287
 aligned with RIR2B_HUMAN | Q7LG56 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:287
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       
          RIR2B_HUMAN    28 KSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMEN 314
               SCOP domains d4djna_ A: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhh........hhhhhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----S------------------------------R---------------------------------------------H----L-----H------------------------------------------------------------------------G-----------------------------S-----------F---------------------------------------------I-------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4djn A  28 KSNEEPLLRKSSRRFVIFPIQYPDIWKmYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEmYSLLIDTYIRDPKKREFLFNAIETmPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLmPGLTFSNELISRDEGLHCDFACLmFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGmNCILmKQYIEFVADRLLVELGFSKVFQAENPFDFmEN 314
                                    37        47       |57        67        77        87        97       107       117       127       137       147       157    |  167       177       187       197       207      |217       227       237|      247       257       267       277    |  287       297       307    |  
                                                      55-MSE                                                                           137-MSE                  162-MSE                                             214-MSE                 238-MSE                                277-MSE|                           312-MSE
                                                                                                                                                                                                                                                                                        282-MSE                            

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with RIR2B_HUMAN | Q7LG56 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:287
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       
          RIR2B_HUMAN    27 IKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFME 313
               SCOP domains d4djnb_ B: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....hhhhh......hhhhhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhh Sec.struct. author
             SAPs(SNPs) (1) ------S------------------------------R---------------------------------------------H----L-----H------------------------------------------------------------------------G-----------------------------S-----------F---------------------------------------------I------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------K----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------RIBORED_SMALL    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4djn B  27 IKSNEEPLLRKSSRRFVIFPIQYPDIWKmYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEmYSLLIDTYIRDPKKREFLFNAIETmPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLmPGLTFSNELISRDEGLHCDFACLmFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGmNCILmKQYIEFVADRLLVELGFSKVFQAENPFDFmE 313
                                    36        46        56        66        76        86        96       106       116       126       136|      146       156     | 166       176       186       196       206       216       226       236 |     246       256       266       276|    | 286       296       306     | 
                                                       55-MSE                                                                           137-MSE                  162-MSE                                             214-MSE                 238-MSE                                277-MSE|                           312-MSE
                                                                                                                                                                                                                                                                                         282-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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR2B_HUMAN | Q7LG56)
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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0009200    deoxyribonucleoside triphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate 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:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0006264    mitochondrial DNA replication    The process in which new strands of DNA are synthesized in the mitochondrion.
    GO:1902254    negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway by p53 class mediator.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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.
    GO:0003014    renal system process    A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
    GO:0014075    response to amine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

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        RIR2B_HUMAN | Q7LG562vux 3hf1

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