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(-) Description

Title :  HUMAN HMT1 HNRNP METHYLTRANSFERASE-LIKE 3 (S. CEREVISIAE) PROTEIN
 
Authors :  J. R. Min, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (S
Date :  08 Feb 06  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Methyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, J. R. Min, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Hmt1 Hnrnp Methyltransferase-Like 3 In Complex With Sah.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 3
    ChainsA
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneHRMT1L3, PRMT3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN METHYLTRANSFERASE- LIKE PROTEIN 3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:241 , HIS A:247 , MET A:250 , ARG A:256 , GLY A:280 , CYS A:281 , ILE A:285 , LEU A:286 , ASP A:302 , GLN A:303 , SER A:304 , GLY A:328 , LYS A:329 , ILE A:330 , GLU A:331 , GLU A:346 , MET A:357 , SER A:360 , HOH A:550 , HOH A:552 , HOH A:562 , HOH A:582BINDING SITE FOR RESIDUE SAH A 549

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:376 -Pro A:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024584L440VANM3_HUMANPolymorphism3758805AL457V
2UniProtVAR_030943S470CANM3_HUMANPolymorphism11025585AS487C
3UniProtVAR_024585S508NANM3_HUMANPolymorphism6483700AN525N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024584L440VANM3_HUMANPolymorphism3758805AL457V
2UniProtVAR_030943S470CANM3_HUMANPolymorphism11025585AS487C
3UniProtVAR_024585S508NANM3_HUMANPolymorphism6483700AN525N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024584L440VANM3_HUMANPolymorphism3758805AL457V
2UniProtVAR_030943S470CANM3_HUMANPolymorphism11025585AS487C
3UniProtVAR_024585S508NANM3_HUMANPolymorphism6483700AN525N

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (10, 10)

Asymmetric Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003310791aENSE00002150419chr11:20409076-20409320245ANM3_HUMAN1-10100--
1.1fENST000003310791fENSE00001293242chr11:20409565-20409700136ANM3_HUMAN10-55460--
1.2ENST000003310792ENSE00001797621chr11:20411290-2041137283ANM3_HUMAN55-83290--
1.3bENST000003310793bENSE00001297538chr11:20413757-2041380650ANM3_HUMAN83-99170--
1.4ENST000003310794ENSE00001314511chr11:20414443-20414545103ANM3_HUMAN100-134350--
1.6ENST000003310796ENSE00001291287chr11:20417349-20417508160ANM3_HUMAN134-187540--
1.7bENST000003310797bENSE00001318617chr11:20419123-20419267145ANM3_HUMAN187-235491A:238-25215
1.8ENST000003310798ENSE00001314116chr11:20424465-2042453066ANM3_HUMAN236-257221A:253-27422
1.9bENST000003310799bENSE00001290930chr11:20429457-20429578122ANM3_HUMAN258-298411A:275-31541
1.10ENST0000033107910ENSE00001318398chr11:20448312-20448411100ANM3_HUMAN298-331341A:315-34834
1.11ENST0000033107911ENSE00001294882chr11:20473676-2047375479ANM3_HUMAN332-358271A:349-37527
1.12ENST0000033107912ENSE00001311854chr11:20483526-20483713188ANM3_HUMAN358-420631A:375-43763
1.13ENST0000033107913ENSE00001327931chr11:20486006-2048609287ANM3_HUMAN421-449291A:438-46629
1.14ENST0000033107914ENSE00001291109chr11:20515465-2051551551ANM3_HUMAN450-466171A:467-48317
1.15ENST0000033107915ENSE00001310698chr11:20515713-2051580088ANM3_HUMAN467-496301A:484-51330
1.16bENST0000033107916bENSE00002195347chr11:20529850-20530799950ANM3_HUMAN496-531361A:513-54836

(-) 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:311
 aligned with ANM3_HUMAN | O60678 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:311
                                   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 
           ANM3_HUMAN   221 FSSYGHYGIHEEMLKDKIRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDVIISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNKHADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIKHIDCHTTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTVFLLEKPFSVKAGEALKGKVTVHKSKKDPRSLTVTLTLNNSTQTYGLQ 531
               SCOP domains d2fyta1 A:238-548 Protein arginine N-methyltransferase 3, PRMT3                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2fytA01 A:238-377 Vaccinia Virus protein VP39                                                                                               -2fytA02 A:379-548 Hnrnp arginine n-methyltransferase1                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee............eeeeee..........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh.....hhhhhhhhh...eee..hhhhh....eeeeeee....hhhhhheeeeeeee....eeeeeeeeeeeeee.......eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------C-------------------------------------N----------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7b      Exon 1.8              ----------------------------------------Exon 1.10  PDB: A:315-348         Exon 1.11  PDB: A:349-375  --------------------------------------------------------------Exon 1.13  PDB: A:438-466    Exon 1.14        Exon 1.15  PDB: A:484-513     ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.9b  PDB: A:275-315                -----------------------------------------------------------Exon 1.12  PDB: A:375-437 UniProt: 358-420                     ---------------------------------------------------------------------------Exon 1.16b  PDB: A:513-548           Transcript 1 (2)
                 2fyt A 238 FSSYGHYGIHEEMLKDKIRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDVIISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNKHADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIKHIDCHTTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTVFLLEKPFSVKAGEALKGKVTVHKNKKDPRSLTVTLTLNNSTQTYGLQ 548
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547 

   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 Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FYT)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (ANM3_HUMAN | O60678)
molecular function
    GO:0008469    histone-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine.
    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: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:0016274    protein-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine.
    GO:0035242    protein-arginine omega-N asymmetric methyltransferase activity    Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues.
    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:0034969    histone arginine methylation    The modification of a histone by addition of a methyl group to an arginine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0035246    peptidyl-arginine N-methylation    The addition of a methyl group onto a nitrogen atom of an arginine residue in a protein.
    GO:0019919    peptidyl-arginine methylation, to asymmetrical-dimethyl arginine    The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    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:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM3_HUMAN | O606783smq 4hsg 4qqn 4ryl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FYT)