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(-) Description

Title :  CRYSTAL STRUCTURE OF VSET UNDER CONDITION A
 
Authors :  H. Wei, M. M. Zhou
Date :  10 Nov 09  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Set Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wei, M. M. Zhou
Dimerization Of A Viral Set Protein Endows Its Function.
Proc. Natl. Acad. Sci. Usa V. 107 18433 2010
PubMed-ID: 20937900  |  Reference-DOI: 10.1073/PNAS.1009911107

(-) Compounds

Molecule 1 - A612L PROTEIN
    Chains: A, B
    Organism Common: PBCV-1
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:3 , ARG A:5 , GLU A:31 , GLU A:32 , HOH A:169 , HOH A:204 , MET B:1 , PHE B:2 , ASN B:3 , GOL B:120 , HOH B:127BINDING SITE FOR RESIDUE GOL A 120
2AC2SOFTWARETYR A:50 , ALA A:82 , HOH A:151 , HOH A:200 , ARG B:38BINDING SITE FOR RESIDUE SO4 A 121
3AC3SOFTWAREILE A:36 , ARG A:38 , HOH A:147 , TYR B:50 , HOH B:125BINDING SITE FOR RESIDUE SO4 A 122
4AC4SOFTWAREGLY A:44 , GLY B:44 , HOH B:128BINDING SITE FOR RESIDUE CL A 123
5AC5SOFTWAREPHE A:2 , ASN A:3 , GOL A:120 , ASN B:3 , GLU B:31 , GLY B:63 , PHE B:64 , HOH B:127 , HOH B:171BINDING SITE FOR RESIDUE GOL B 120

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KMA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KMA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KMA)

(-) Exons   (0, 0)

(no "Exon" information available for 3KMA)

(-) 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:105
 aligned with O41094_PBCV1 | O41094 from UniProtKB/TrEMBL  Length:119

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
         O41094_PBCV1     1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISY 105
               SCOP domains d3kmaa_ A: Viral histone H3 Lysine 27 Methyltransferase                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeee........eeeeeeeeeee.hhh........eee..eeeee.......ee.....eeeee.....eeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3kma A   1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISY 105
                                    10        20        30        40        50        60        70        80        90       100     


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with O41094_PBCV1 | O41094 from UniProtKB/TrEMBL  Length:119

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
         O41094_PBCV1     1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISY 105
               SCOP domains d3kmab_ B: Viral histone H3 Lysine 27 Methyltransferase                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------SET-3kmaB01 B:43-105                                            Pfam domains (1)
           Pfam domains (2) ------------------------------------------SET-3kmaB02 B:43-105                                            Pfam domains (2)
         Sec.struct. author .....eeeee.....eeeee........eeeeeeeeeee.hhh........eee..eeeee.......ee.....eeeee.....eeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3kma B   1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISY 105
                                    10        20        30        40        50        60        70        80        90       100
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SET] (46)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O41094_PBCV1 | O41094)
molecular function
    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).
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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 Related Entries

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

UniProtKB/TrEMBL
        O41094_PBCV1 | O41094: 1n3j 2g46 3kmj 3kmt

(-) Related Entries Specified in the PDB File

3kmj CRYSTAL STRUCTURE OF VSET UNDER CONDITION B
3kmt CRYSTAL STRUCTURE OF VSET/SAH/H3 TERNARY COMPLEX