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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAH (MONOCLINIC FORM 2)
 
Authors :  R. Assenberg, J. Ren, A. Verma, T. S. Walter, D. Alderton, R. J. Hurrelbr S. D. Fuller, R. J. Owens, D. I. Stuart, J. M. Grimes, Oxford Protein P Facility (Oppf)
Date :  14 May 07  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Murray Valley Encephalitis Virus, Methyltransferase, Sah, Structural Genomics, Oxford Protein Production Facility, Oppf, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Assenberg, J. Ren, A. Verma, T. S. Walter, D. Alderton, R. J. Hurrelbrink, S. D. Fuller, S. Bressanelli, R. J. Owens, D. I. Stuart, J. M. Grimes
Crystal Structure Of The Murray Valley Encephalitis Virus Ns5 Methyltransferase Domain In Complex With Cap Analogues.
J. Gen. Virol. V. 88 2228 2007
PubMed-ID: 17622627  |  Reference-DOI: 10.1099/VIR.0.82757-0

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN [CONTAINS: CAPSID PROTEIN C (CORE PROTEIN)
    ChainsA
    EC Number2.7.7.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidOPPF2936
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNS5
    Organism ScientificMURRAY VALLEY ENCEPHALITIS VIRUS (STRAIN MVE-1- 51)
    Organism Taxid301478
    StrainMVE-1-51, MVEV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO47Ligand/IonSULFATE ION
5UNX9Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:119 , ALA A:266BINDING SITE FOR RESIDUE CL A 890
02AC2SOFTWAREGLY A:52 , ASN A:259 , LEU A:260 , GLY A:261BINDING SITE FOR RESIDUE CL A 925
03AC3SOFTWAREGLU A:149 , HOH A:930BINDING SITE FOR RESIDUE CL A 894
04AC4SOFTWAREARG A:37 , ARG A:41 , SER A:56 , ARG A:57 , ARG A:84 , HOH A:979BINDING SITE FOR RESIDUE SO4 A 601
05AC5SOFTWAREARG A:57 , LYS A:61 , LEU A:211 , SER A:212 , ARG A:213 , ASN A:216 , GLU A:218 , SO4 A:606BINDING SITE FOR RESIDUE SO4 A 602
06AC6SOFTWAREARG A:63 , VAL A:258 , ASN A:259 , HOH A:959 , HOH A:972BINDING SITE FOR RESIDUE SO4 A 603
07AC7SOFTWAREGLY A:203 , GLY A:204 , SER A:223 , HOH A:994 , HOH A:1044BINDING SITE FOR RESIDUE SO4 A 604
08AC8SOFTWAREARG A:243 , HOH A:917 , HOH A:945 , HOH A:1043BINDING SITE FOR RESIDUE SO4 A 605
09AC9SOFTWAREPHE A:24 , ARG A:28 , ARG A:213 , SER A:215 , SO4 A:602 , HOH A:949BINDING SITE FOR RESIDUE SO4 A 606
10BC1SOFTWAREARG A:84 , GLU A:111 , GLU A:112 , HOH A:920 , HOH A:992BINDING SITE FOR RESIDUE SO4 A 607
11BC2SOFTWAREASP A:170 , UNX A:802 , UNX A:803 , UNX A:806 , HOH A:1007BINDING SITE FOR RESIDUE UNX A 801
12BC3SOFTWARESER A:137 , MET A:167 , ASP A:170 , TRP A:171 , UNX A:801 , UNX A:803 , HOH A:914BINDING SITE FOR RESIDUE UNX A 802
13BC4SOFTWARESER A:137 , ASP A:170 , UNX A:801 , UNX A:802 , UNX A:804BINDING SITE FOR RESIDUE UNX A 803
14BC5SOFTWAREGLU A:22 , SER A:137 , UNX A:803BINDING SITE FOR RESIDUE UNX A 804
15BC6SOFTWAREPHE A:133 , UNX A:807 , UNX A:808 , UNX A:809BINDING SITE FOR RESIDUE UNX A 805
16BC7SOFTWAREASP A:170 , UNX A:801 , UNX A:809BINDING SITE FOR RESIDUE UNX A 806
17BC8SOFTWAREPHE A:133 , UNX A:805BINDING SITE FOR RESIDUE UNX A 807
18BC9SOFTWAREARG A:163 , UNX A:805 , UNX A:809BINDING SITE FOR RESIDUE UNX A 808
19CC1SOFTWAREPHE A:133 , UNX A:805 , UNX A:806 , UNX A:808BINDING SITE FOR RESIDUE UNX A 809
20CC2SOFTWARESER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:83 , GLY A:86 , TRP A:87 , LYS A:105 , HIS A:110 , GLU A:111 , VAL A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , HOH A:892 , HOH A:896 , HOH A:909BINDING SITE FOR RESIDUE SAH A 500
21CC3SOFTWAREGLU A:22 , GLU A:23 , SER A:173 , TRP A:249 , HOH A:1031 , HOH A:1036BINDING SITE FOR RESIDUE GOL A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PX4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PX4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PX4)

(-) Exons   (0, 0)

(no "Exon" information available for 2PX4)

(-) 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:261
 aligned with POLG_MVEV5 | P05769 from UniProtKB/Swiss-Prot  Length:3434

    Alignment length:263
                                  2544      2554      2564      2574      2584      2594      2604      2614      2624      2634      2644      2654      2664      2674      2684      2694      2704      2714      2724      2734      2744      2754      2764      2774      2784      2794   
          POLG_MVEV5   2535 RTLGEQWKEKLNAMGKEEFFSYRKEAILEVDRTEARRARREGNKVGGHPVSRGTAKLRWLVERRFVQPIGKVVDLGCGRGGWSYYAATMKNVQEVRGYTKGGPGHEEPMLMQSYGWNIVTMKSGVDVFYKPSEISDTLLCDIGESSPSAEIEEQRTLRILEMVSDWLSRGPKEFCIKILCPYMPKVIEKLESLQRRFGGGLVRVPLSRNSNHEMYWVSGASGNIVHAVNMTSQVLIGRMDKKIWKGPKYEEDVNLGSGTRAVG 2797
               SCOP domains d2px4a_ A: An RNA cap (nucleoside-2'-O-)-  methyltransferase domain of RNA polymerase NS5                                                                                                                                                                               SCOP domains
               CATH domains 2px4A00 A:6-268 Vaccinia Virus protein VP  39                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------FtsJ-2px4A01 A:54-225                                                                                                                                                       ---------------------------Flavi_NS5-2px4A0 Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh...eee.hhhhhh....--........hhhhhhhhhhhh......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhh.........eee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2px4 A    6 RTLGEQWKEKLNAMGKEEFFSYRKEAILEVDRTEARRARRE--KVGGHPVSRGTAKLRWLVERRFVQPIGKVVDLGCGRGGWSYYAATMKNVQEVRGYTKGGPGHEEPMLMQSYGWNIVTMKSGVDVFYKPSEISDTLLCDIGESSPSAEIEEQRTLRILEMVSDWLSRGPKEFCIKILCPYMPKVIEKLESLQRRFGGGLVRVPLSRNSNHEMYWVSGASGNIVHAVNMTSQVLIGRMDKKIWKGPKYEEDVNLGSGTRAVG  268
                                    15        25        35        45|  |    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
                                                                   46 49                                                                                                                                                                                                                           

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: RdRP (210)

(-) Gene Ontology  (60, 60)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POLG_MVEV5 | P05769)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    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:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0004482    mRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. m7G(5')pppR-RNA is mRNA containing an N7-methylguanine cap; R may be guanosine or adenosine.
    GO:0004483    mRNA (nucleoside-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0070008    serine-type exopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0016070    RNA metabolic process    The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0080009    mRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0044167    host cell endoplasmic reticulum membrane    The lipid bilayer surrounding the host cell endoplasmic reticulum.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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

UniProtKB/Swiss-Prot
        POLG_MVEV5 | P057692px2 2px5 2px8 2pxa 2pxc 2v8o 2wv9

(-) Related Entries Specified in the PDB File

2px2 CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAH (MONOCLINIC FORM 1)
2px5 CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAH (ORTHORHOMBIC CRYSTAL FORM)
2px8 CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAH AND 7M-GTP
2pxa CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAH AND GTPG
2pxc CRYSTAL STRUCTURE OF THE MURRAY VALLEY ENCEPHALITIS VIRUS NS5 2'-O METHYLTRANSFERASE DOMAIN IN COMPLEX WITH SAM AND GTPA