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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MKP-2
 
Authors :  D. G. Jeong, S. K. Jung, S. E. Ryu, S. J. Kim
Date :  24 Oct 08  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (4x),B (4x),C (4x),D (4x),E (4x),F (4x)
Keywords :  Alpha/Beta, Hydrolase, Nucleus, Protein Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. G. Jeong, S. K. Jung, T. S. Yoon, E. J. Woo, J. H. Kim, B. C. Park, S. E. Ryu, S. J. Kim
Crystal Structure Of The Catalytic Domain Of Human Mkp-2 Reveals A 24-Mer Assembly.
Proteins V. 76 763 2009
PubMed-ID: 19415758  |  Reference-DOI: 10.1002/PROT.22423
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN PHOSPHATASE 4
    ChainsA, B, C, D, E, F
    EC Number3.1.3.48, 3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GeneDUSP4, MKP2, VH2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 2, MAP KINASE PHOSPHATASE 2, MKP-2, DUAL SPECIFICITY PROTEIN PHOSPHATASE HVH2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (4x)A (4x)B (4x)C (4x)D (4x)E (4x)F (4x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1SO420Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:249 , SER A:280 , GLN A:281 , ALA A:282 , GLY A:283 , ILE A:284 , SER A:285 , ARG A:286BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWARESER B:280 , GLN B:281 , ALA B:282 , GLY B:283 , ILE B:284 , SER B:285 , ARG B:286BINDING SITE FOR RESIDUE SO4 B 502
3AC3SOFTWAREASP C:249 , SER C:280 , GLN C:281 , ALA C:282 , GLY C:283 , ILE C:284 , SER C:285 , ARG C:286BINDING SITE FOR RESIDUE SO4 C 503
4AC4SOFTWAREASP D:249 , SER D:280 , GLN D:281 , ALA D:282 , GLY D:283 , ILE D:284 , SER D:285 , ARG D:286BINDING SITE FOR RESIDUE SO4 D 504
5AC5SOFTWARESER E:280 , GLN E:281 , ALA E:282 , GLY E:283 , ILE E:284 , SER E:285 , ARG E:286BINDING SITE FOR RESIDUE SO4 E 505
6AC6SOFTWARESER F:280 , GLN F:281 , ALA F:282 , GLY F:283 , ILE F:284 , SER F:285 , ARG F:286BINDING SITE FOR RESIDUE SO4 F 506
7AC7SOFTWAREARG A:214BINDING SITE FOR RESIDUE SO4 A 507
8AC8SOFTWAREARG D:214BINDING SITE FOR RESIDUE SO4 D 508
9AC9SOFTWAREARG B:214 , ARG C:214 , ARG E:214 , ARG F:214BINDING SITE FOR RESIDUE SO4 C 509

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 18)

Asymmetric Unit (3, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS4_HUMAN195-335
 
 
 
 
 
  6A:195-335
B:195-335
C:195-335
D:195-335
E:195-335
F:195-335
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS4_HUMAN263-314
 
 
 
 
 
  6A:263-314
B:263-314
C:263-314
D:263-314
E:263-314
F:263-314
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS4_HUMAN278-288
 
 
 
 
 
  6A:278-288
B:278-288
C:278-288
D:278-288
E:278-288
F:278-288
Biological Unit 1 (3, 72)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS4_HUMAN195-335
 
 
 
 
 
  24A:195-335
B:195-335
C:195-335
D:195-335
E:195-335
F:195-335
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS4_HUMAN263-314
 
 
 
 
 
  24A:263-314
B:263-314
C:263-314
D:263-314
E:263-314
F:263-314
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS4_HUMAN278-288
 
 
 
 
 
  24A:278-288
B:278-288
C:278-288
D:278-288
E:278-288
F:278-288

(-) Exons   (0, 0)

(no "Exon" information available for 3EZZ)

(-) 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:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezza_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: A:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz A 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezzb_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: B:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz B 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezzc_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: C:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz C 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezzd_ D: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: D:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: D:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz D 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

Chain E from PDB  Type:PROTEIN  Length:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezze_ E: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: E:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: E:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz E 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

Chain F from PDB  Type:PROTEIN  Length:144
 aligned with DUS4_HUMAN | Q13115 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:144
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           DUS4_HUMAN   193 QGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHCQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
               SCOP domains d3ezzf_ F: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeeehhhhhhhhhhhhh...eeee.............eeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TYR_PHOSPHATASE_DUAL  PDB: F:195-335 UniProt: 195-335                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: F:263-314 UniProt: 263-314  ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ezz F 193 MGGPVEILPFLYLGSAYHAARRDMLDALGITALLNVSSDCPNHFEGHYQYKCIPVEDNHKADISSWFMEAIEYIDAVKDCRGRVLVHSQAGISRSATICLAYLMMKKRVRLEEAFEFVKQRRSIISPNFSFMGQLLQFESQVLA 336
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332    

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (DUS4_HUMAN | Q13115)
molecular function
    GO:0017017    MAP kinase tyrosine/serine/threonine phosphatase activity    Catalysis of the reaction: MAP kinase serine/threonine/tyrosine phosphate + H2O = MAP kinase serine/threonine/tyrosine + phosphate.
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008330    protein tyrosine/threonine phosphatase activity    Catalysis of the reactions: protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0001706    endoderm formation    The formation of the endoderm during gastrulation.
    GO:0000188    inactivation of MAPK activity    Any process that terminates the activity of the active enzyme MAP kinase.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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