Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF LYS42 ACETYLATED HUMAN SUMO2
 
Authors :  M. T. Naik, N. Naik, H. Shih, T. Huang
Date :  19 Jun 16  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Ubiquitin-Like Protein, Acetylated Protein, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Naik, N. Naik, H. Shih, T. Huang
Structures Of Human Sumo
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SMALL UBIQUITIN-RELATED MODIFIER 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PCDFDUET-1
    Expression System Vector Type: PCDFDUET-1
    Fragment: UNP RESIDUES 1-93
    Gene: SUMO2, SMT3B, SMT3H2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LYS42 ACETYLATED MATURE SMALL UBIQUITIN-RELATED MODIFIER 2 (SUMO2) RESIDUES 1-14 (MGSSHHHHHHSQDP) REPRESENT A NON- NATIVE PURIFICATION TAG. THESE RESIDUES WERE NEITHER ASSIGNED NOR INCLUDED IN STRUCTURE CALCULATION.
    Other Details - Source: PLASMID PCDF PYLT-1 WITH SUMO INSERT WITH K42STOP MUTATION (WITH AMBER CODON) AND PACKRS-3 AS DESCRIBED IN NEUMANN ET AL., MOL CELL, 36, 153, 2009
    Synonym: SUMO-2,HSMT3,SMT3 HOMOLOG 2,SUMO-3,SENTRIN-2,UBIQUITIN-LIKE PROTEIN SMT3B,SMT3B

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 5GHB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GHB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GHB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GHB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GHB)

(-) Exons   (0, 0)

(no "Exon" information available for 5GHB)

(-) Sequences/Alignments

NMR Structure
   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:93
                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeee.....eeeeeee...hhhhhhhhhhhhhh.hhhhheeee..ee...............eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  5ghb A  1 MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSkLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG 93
                                    10        20        30        40 |      50        60        70        80        90   
                                                                    42-ALY
   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 5GHB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GHB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GHB)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ALY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5ghb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ghb)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ghb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SUMO2_HUMAN | P61956
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SUMO2_HUMAN | P61956
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SUMO2_HUMAN | P61956: 1wm2 1wm3 1wz0 1z5q 2awt 2ckh 2d07 2io0 2io3 2iyd 2n1w 2n9e 2rpq 3uin 3uio 3zo5 4bkg 4npn 5d2m 5elu 5eql 5ghc

(-) Related Entries Specified in the PDB File

2n1w RELATED ID: 36006 RELATED DB: BMRB
5b7a
5ghc
5ghd