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(-) Description

Title :  HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE
 
Authors :  J. Yuvaniyama, J. M. Denu, J. E. Dixon, M. A. Saper
Date :  20 Feb 96  (Deposition) - 20 Jun 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Protein Dual-Specificity Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Yuvaniyama, J. M. Denu, J. E. Dixon, M. A. Saper
Crystal Structure Of The Dual Specificity Protein Phosphatase Vhr.
Science V. 272 1328 1996
PubMed-ID: 8650541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7-VHR
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsORIGINAL GENE GDB:DUSP3;
VHR, CHROMOSOME MAP POSITION 17Q21
    SynonymVHR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:92 , CYS B:124 , ARG B:125 , GLU B:126 , GLY B:127 , TYR B:128 , SER B:129 , ARG B:130 , HOH B:657BINDING SITE FOR RESIDUE SO4 B 502
02AC2SOFTWAREASP A:92 , CYS A:124 , ARG A:125 , GLU A:126 , GLY A:127 , TYR A:128 , SER A:129 , ARG A:130BINDING SITE FOR RESIDUE EPE A 401
03GAAUNKNOWNILE A:88 , LYS A:89 , ALA A:90 , ASN A:91 , ASP A:92 , THR A:93 , GLN A:94 , GLU A:95 , PHE A:96 , ASN A:97 , LEU A:98THE LOOP CONTAINING THE PUTATIVE GENERAL ACID ASP 92.
04GABUNKNOWNILE B:88 , LYS B:89 , ALA B:90 , ASN B:91 , ASP B:92 , THR B:93 , GLN B:94 , GLU B:95 , PHE B:96 , ASN B:97 , LEU B:98THE LOOP CONTAINING THE PUTATIVE GENERAL ACID ASP 92.
05PLAUNKNOWNHIS A:123 , CYS A:124 , ARG A:125 , GLU A:126 , GLY A:127 , TYR A:128 , SER A:129 , ARG A:130 , SER A:131PHOSPHATE BINDING LOOP INCLUDING CATALYTIC NUCLEOPHILE CYS 130
06PLBUNKNOWNHIS B:123 , CYS B:124 , ARG B:125 , GLU B:126 , GLY B:127 , TYR B:128 , SER B:129 , ARG B:130 , SER B:131PHOSPHATE BINDING LOOP INCLUDING CATALYTIC NUCLEOPHILE CYS 130
07RCAUNKNOWNGLY A:19 , SER A:20 , GLY A:21 , CYS A:22 , TYR A:23 , SER A:24 , LEU A:25 , PRO A:26 , SER A:27 , GLN A:28 , PRO A:29DESIGNATED RECOGNITION REGION IN PRIMARY REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.
08RCBUNKNOWNGLY B:19 , SER B:20 , GLY B:21 , CYS B:22 , TYR B:23 , SER B:24 , LEU B:25 , PRO B:26 , SER B:27 , GLN B:28 , PRO B:29DESIGNATED RECOGNITION REGION IN PRIMARY REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.
09VRAUNKNOWNALA A:62 , ALA A:63 , GLU A:64 , GLY A:65 , ARG A:66 , SER A:67 , PHE A:68 , MET A:69 , HIS A:70 , VAL A:71 , ASN A:72 , THR A:73 , ASN A:74 , ALA A:75 , ASN A:76 , PHE A:77 , TYR A:78 , LYS A:79 , ASP A:80 , SER A:81 , GLY A:82THE REGION CONTAINING HIGH VARIATION AMONG THE DUAL-SPECIFICITY PHOSPHATASES AND THE PROTEIN TYROSINE PHOSPHATASES.
10VRBUNKNOWNALA B:62 , ALA B:63 , GLU B:64 , GLY B:65 , ARG B:66 , SER B:67 , PHE B:68 , MET B:69 , HIS B:70 , VAL B:71 , ASN B:72 , THR B:73 , ASN B:74 , ALA B:75 , ASN B:76 , PHE B:77 , TYR B:78 , LYS B:79 , ASP B:80 , SER B:81 , GLY B:82THE REGION CONTAINING HIGH VARIATION AMONG THE DUAL-SPECIFICITY PHOSPHATASES AND THE PROTEIN TYROSINE PHOSPHATASES.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VHR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VHR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VHR)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS3_HUMAN32-178
 
  2A:32-178
B:32-178
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS3_HUMAN99-158
 
  2A:99-158
B:99-158
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS3_HUMAN122-132
 
  2A:122-132
B:122-132
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS3_HUMAN32-178
 
  1A:32-178
-
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS3_HUMAN99-158
 
  1A:99-158
-
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS3_HUMAN122-132
 
  1A:122-132
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_DUALPS50054 Dual specificity protein phosphatase family profile.DUS3_HUMAN32-178
 
  1-
B:32-178
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.DUS3_HUMAN99-158
 
  1-
B:99-158
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.DUS3_HUMAN122-132
 
  1-
B:122-132

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002260041ENSE00000854206chr17:41856368-41856168201DUS3_HUMAN1-42422A:8-42
B:8-42
35
35
1.2ENST000002260042ENSE00000731379chr17:41852306-41852080227DUS3_HUMAN42-118772A:42-118
B:42-118
77
77
1.3ENST000002260043ENSE00001292277chr17:41847182-418434903693DUS3_HUMAN118-185682A:118-185
B:118-185
68
68

(-) 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:178
 aligned with DUS3_HUMAN | P51452 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:178
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177        
           DUS3_HUMAN     8 SVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP 185
               SCOP domains d1vhra_ A: VH1-related dual-specificity phosphatase, VHR                                                                                                                           SCOP domains
               CATH domains 1vhrA00 A:8-185 Protein tyrosine phosphatase superfamily                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee..eeee.hhhh..hhhhhhh...eeee.............hhhh.....eeee..........hhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------TYR_PHOSPHATASE_DUAL  PDB: A:32-178 UniProt: 32-178                                                                                                ------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:99-158 UniProt: 99-158            --------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1  PDB: A:8-42 UniProt: 1-42---------------------------------------------------------------------------Exon 1.3  PDB: A:118-185 UniProt: 118-185                            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.2  PDB: A:42-118 UniProt: 42-118                                      ------------------------------------------------------------------- Transcript 1 (2)
                 1vhr A   8 SVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP 185
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177        

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with DUS3_HUMAN | P51452 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:178
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177        
           DUS3_HUMAN     8 SVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP 185
               SCOP domains d1vhrb_ B: VH1-related dual-specificity phosphatase, VHR                                                                                                                           SCOP domains
               CATH domains 1vhrB00 B:8-185 Protein tyrosine phosphatase superfamily                                                                                                                           CATH domains
           Pfam domains (1) -----------------------------DSPc-1vhrB01 B:37-176                                                                                                                       --------- Pfam domains (1)
           Pfam domains (2) -----------------------------DSPc-1vhrB02 B:37-176                                                                                                                       --------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh.............eeeee..eeee.hhhh..hhhhhh....eeee......................eeee..........hhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------TYR_PHOSPHATASE_DUAL  PDB: B:32-178 UniProt: 32-178                                                                                                ------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:99-158 UniProt: 99-158            --------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1  PDB: B:8-42 UniProt: 1-42---------------------------------------------------------------------------Exon 1.3  PDB: B:118-185 UniProt: 118-185                            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.2  PDB: B:42-118 UniProt: 42-118                                      ------------------------------------------------------------------- Transcript 1 (2)
                 1vhr B   8 SVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP 185
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: DSPc (22)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DUS3_HUMAN | P51452)
molecular function
    GO:0033549    MAP kinase phosphatase activity    Catalysis of the reaction: a phosphorylated MAP kinase + H2O = a MAP kinase + 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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0000188    inactivation of MAPK activity    Any process that terminates the activity of the active enzyme MAP kinase.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0046329    negative regulation of JNK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043409    negative regulation of MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
    GO:0050868    negative regulation of T cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0045931    positive regulation of mitotic cell cycle    Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    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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        DUS3_HUMAN | P514521j4x 3f81

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