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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIBONUCLEOTIDE REDUCTASE 1 BOUND TO THE EFFECTOR TTP
 
Authors :  J. W. Fairman, S. R. Wijerathna, H. Xu, C. G. Dealwis
Date :  31 May 09  (Deposition) - 23 Feb 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Ribonucleotide Reductase, Allosteric Enzyme, Atp- Binding, Dna Replication, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Fairman, S. R. Wijerathna, M. F. Ahmad, H. Xu, R. Nakano, S. Jha, J. Prendergast, R. M. Welin, S. Flodin, A. Roos, P. Nordlund, Z. Li, T. Walz, C. G. Dealwis
Structural Basis For Allosteric Regulation Of Human Ribonucleotide Reductase By Nucleotide-Induced Oligomerization.
Nat. Struct. Mol. Biol. V. 18 316 2011
PubMed-ID: 21336276  |  Reference-DOI: 10.1038/NSMB.2007

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT
    ChainsA, B
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRR1, RRM1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M1, RIBONUCLEOTIDE REDUCTASE LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO46Ligand/IonSULFATE ION
3TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETTP A:802 , HOH A:921BINDING SITE FOR RESIDUE MG A 801
02AC2SOFTWAREASP A:226 , SER A:227 , ILE A:228 , ILE A:231 , ARG A:256 , ILE A:262 , ALA A:263 , GLY A:264 , SER A:269 , ASN A:270 , HOH A:793 , MG A:801 , HOH A:921 , LYS B:243 , TYR B:285 , VAL B:286 , ASP B:287 , GLN B:288 , GLY B:289BINDING SITE FOR RESIDUE TTP A 802
03AC3SOFTWAREILE A:136 , TYR A:137 , ASP A:138 , HOH A:982 , LYS B:382BINDING SITE FOR RESIDUE SO4 A 804
04AC4SOFTWARESER A:687 , GLN A:688 , LYS A:689BINDING SITE FOR RESIDUE SO4 A 805
05AC5SOFTWAREALA A:201 , SER A:202 , THR A:604 , SER A:606 , THR A:607 , HOH A:826 , HOH A:860 , HOH A:892 , HOH A:919BINDING SITE FOR RESIDUE SO4 A 809
06AC6SOFTWARETTP B:802 , HOH B:919BINDING SITE FOR RESIDUE MG B 801
07AC7SOFTWARELYS A:243 , TYR A:285 , VAL A:286 , ASP A:287 , GLN A:288 , ASP B:226 , SER B:227 , ILE B:228 , ILE B:231 , ILE B:255 , ARG B:256 , ILE B:262 , ALA B:263 , GLY B:264 , SER B:269 , ASN B:270 , HOH B:793 , MG B:801 , HOH B:805 , HOH B:919BINDING SITE FOR RESIDUE TTP B 802
08AC8SOFTWARESER B:687 , GLN B:688 , LYS B:689 , HOH B:873 , HOH B:968 , HOH B:969BINDING SITE FOR RESIDUE SO4 B 803
09AC9SOFTWARELYS B:5 , ARG B:6 , THR B:53 , HOH B:970BINDING SITE FOR RESIDUE SO4 B 806
10BC1SOFTWARESER B:202 , PRO B:603 , THR B:604 , ALA B:605 , SER B:606 , THR B:607 , HOH B:956BINDING SITE FOR RESIDUE SO4 B 807

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HNC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:402 -Pro A:403
2Thr B:402 -Pro B:403

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052052K590QRIR1_HUMANPolymorphism2228123A/BK590Q

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_HUMAN1-92  1B:1-92
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_HUMAN581-603
 
  2A:581-603
B:581-603

(-) Exons   (0, 0)

(no "Exon" information available for 3HNC)

(-) 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:714
 aligned with RIR1_HUMAN | P23921 from UniProtKB/Swiss-Prot  Length:792

    Alignment length:729
                                    23        33        43        53        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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733         
           RIR1_HUMAN    14 MFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR 742
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeehhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhhh..eeeee.........ee....ee...hhhhhhhhhhhhhhh..------..eeeee.....hhhhhh....---------..eeeeeeehhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhh..eeeehhhhhhh..hhhhh....................eee.eeeee.hhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhh........hhhhhhhhhhhhh...........hhhhhhhhh...........eeeeee..eeeeeehhhhhhhhhhh...hhhhhhhhhhh..........hhhhhhhh......hhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhhhh...eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: - UniProt: 1-92                                                 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hnc A  14 MFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQ------GAFAIYLEPWHLDIFEFLDLKK---------RDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR 742
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283    |    - |     303       313  |      -  |    333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733         
                                                                                                                                                                                                                                                                                                            288    295                  316       326                                                                                                                                                                                                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:738
 aligned with RIR1_HUMAN | P23921 from UniProtKB/Swiss-Prot  Length:792

    Alignment length:742
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740  
           RIR1_HUMAN     1 MHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR 742
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee.hhhhhhhhhhh..........hhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeehhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhhh..eeeee.........ee....ee..hhhhhhhhhhhhhhhh.....--...eeeee.....hhhhhh................eeeeeehhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhh..eeeehhhhhhh..hhhhh....................eee.eeeee.hhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.hhhhhh........hhhhhhhhhhhhh...........hhhhhhhhh...........eeee..--..eeeehhhhhhhhhhh...hhhhhhhhhh...........hhhhhhhh......hhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhhhhh..eee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: B:1-92 UniProt: 1-92                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hnc B   1 MHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGN--PGAFAIYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRV--GEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR 742
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290|  |   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620        |- |     640       650       660       670       680       690       700       710       720       730       740  
                                                                                                                                                                                                                                                                                                                            291  |                                                                                                                                                                                                                                                                                                                                            629  |                                                                                                              
                                                                                                                                                                                                                                                                                                                               294                                                                                                                                                                                                                                                                                                                                               632                                                                                                              

   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 3HNC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HNC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HNC)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR1_HUMAN | P23921)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0017076    purine nucleotide binding    Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate.
    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:0021846    cell proliferation in forebrain    The creation of greater cell numbers in the forebrain due to cell division of progenitor cells.
    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:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    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:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0010212    response to ionizing radiation    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 a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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        RIR1_HUMAN | P239212wgh 3hnd 3hne 3hnf 4x3v 5d1y

(-) Related Entries Specified in the PDB File

3hnd CRYSTAL STRUCTURE OF HUMAN RIBONUCLEOTIDE REDUCTASE 1 BOUND TO THE EFFECTOR TTP AND SUBSTRATE GDP
3hne CRYSTAL STRUCTURE OF HUMAN RIBONUCLEOTIDE REDUCTASE 1 BOUND TO THE EFFECTORS TTP AND ATP
3hnf CRYSTAL STRUCTURE OF HUMAN RIBONUCLEOTIDE REDUCTASE 1 BOUND TO THE EFFECTORS TTP AND DATP