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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC UNCOMPLEXED FORM OF XENOPUS DISHEVELLED PDZ DOMAIN
 
Authors :  N. Friedland, L. -W. Hung, B. Cheyette, R. T. Moon, T. N. Earnest
Date :  12 Nov 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Biol. Unit 6:  A (1x),B (1x),D (1x)
Biol. Unit 7:  B,D  (1x)
Keywords :  Dishevelled, Pdz Domain, Monomer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Friedland, L. -W. Hung, B. Cheyette, J. R. Miller, R. T. Moon, T. N. Earnest
Conformational Flexibility In The Pdz Domain Of Dishevelled Induced By Target Binding
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL- 2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21B
    Expression System StrainN834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDISHEVELLED PDZ DOMAIN
    GeneDVL2
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
    SynonymDISHEVELLED-2, DSH HOMOLOG 2, XDSH

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)ABCD
Biological Unit 6 (1x)A (1x)B (1x) D (1x)
Biological Unit 7 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 21)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE-1Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 7 (2, 11)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:276 , HIS B:344 , HIS B:346 , HIS D:344 , HIS D:346BINDING SITE FOR RESIDUE CO B 349
2AC2SOFTWAREHIS A:329 , HOH D:56 , HOH D:138 , THR D:256 , ARG D:297BINDING SITE FOR RESIDUE SO4 D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F0A)

(-) PROSITE Motifs  (2, 5)

Asymmetric Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  4A:254-326
B:254-326
C:254-326
D:254-326
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  1B:345-346
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  1A:254-326
-
-
-
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  0-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  1-
B:254-326
-
-
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  1B:345-346
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  1-
-
C:254-326
-
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  0-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  1-
-
-
D:254-326
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  0-
Biological Unit 5 (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  4A:254-326
B:254-326
C:254-326
D:254-326
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  1B:345-346
Biological Unit 6 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  3A:254-326
B:254-326
-
D:254-326
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  1B:345-346
Biological Unit 7 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DVL2_XENLA254-326
 
 
 
  2-
B:254-326
-
D:254-326
2DEPPS50186 DEP domain profile.DVL2_XENLA428-502  1B:345-346

(-) Exons   (0, 0)

(no "Exon" information available for 2F0A)

(-) 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:92
 aligned with DVL2_XENLA | P51142 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:92
                                   260       270       280       290       300       310       320       330       340  
           DVL2_XENLA   251 NIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDIVHKPGPIVLTVAKCW 342
               SCOP domains d2f0aa_ A: Segment polarity protein dishevelled homolog Dvl-2                                SCOP domains
               CATH domains -2f0aA00 A:252-342  [code=2.30.42.10, no name defined]                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhh...eeee..........eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:254-326 UniProt: 254-326                                     ---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2f0a A 251 mIITVTLNmEKYNFLGISIVGQSNERGDGGIYIGSImKGGAVAADGRIEPGDmLLQVNDINFENmSNDDAVRVLRDIVHKPGPIVLTVAKLE 342
                            |      260       270       280      |290       300  |    310    |  320       330       340  
                            |     259-MSE                     287-MSE         303-MSE     315-MSE                       
                          251-MSE                                                                                       

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with DVL2_XENLA | P51142 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:210
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
           DVL2_XENLA   251 NIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDIVHKPGPIVLTVAKCWDPSPQGYFTLPRNEPIHPIDPAAWVSHSAALSGSFPVYPGSASMSSMTSSTSVTETELSHALPPVSLFSLSVHTDLASVVKVMASPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHH 460
               SCOP domains d2f0ab_ B: Segment pola      rity protein dishevelled homolog Dvl-2                                                                                                                                                SCOP domains
               CATH domains -2f0aB00 B:252-346  [co      de=2.30.42.10, no name defined]                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhhh...eeeee..------.eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhh...-.eeeeee.-----------------------------------------------------------.ee-------------------------------------------------------e.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---PDZ  PDB: B:254-326 UniProt: 254-326                                     -----------------------------------------------------------------------------------------------------DEP  PDB: B:345-346               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f0a B 251 mIITVTLNmEKYNFLGISIVGQS------GIYIGSImKGGAVAADGRIEPGDmLLQVNDINFENmSNDDAVRVLRDIVHKP-PIVLTVAK-----------------------------------------------------------LEH-------------------------------------------------------HHH 346
                            |      260       270  |    280      |290       300  |    310    |  320       330| |    340         -         -         -         -         -       341 |       -         -         -         -         -       346
                          251-MSE 259-MSE       273    280      |             303-MSE     315-MSE         331 |    340                                                         341 |                                                     344  
                                                              287-MSE                                       333                                                                  343                                                          

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with DVL2_XENLA | P51142 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:90
                                   260       270       280       290       300       310       320       330       340
           DVL2_XENLA   251 NIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDIVHKPGPIVLTVAK 340
               SCOP domains d2f0ac_ C: Segment polar     ity protein dishevelled homolog Dvl-2                         SCOP domains
               CATH domains -2f0aC00 C:252-340  [cod     e=2.30.42.10, no name defined]                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhhh...eeeee...-----.eeeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---PDZ  PDB: C:254-326 UniProt: 254-326                                     -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2f0a C 251 mIITVTLNmEKYNFLGISIVGQSN-----GIYIGSImKGGAVAADGRIEPGDmLLQVNDINFENmSNDDAVRVLRDIVHKPGPIVLTVAK 340
                            |      260       270   |   280      |290       300  |    310    |  320       330       340
                            |     259-MSE        274   280      |             303-MSE     315-MSE                     
                          251-MSE                             287-MSE                                                 

Chain D from PDB  Type:PROTEIN  Length:89
 aligned with DVL2_XENLA | P51142 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:109
                                   260       270       280       290       300       310       320       330       340       350         
           DVL2_XENLA   251 NIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDIVHKPGPIVLTVAKCWDPSPQGYFTLPRNEPIH 359
               SCOP domains d2f0ad_ D: Segment pol       arity protein dishevelled homolog Dvl-2                                          SCOP domains
               CATH domains -2f0aD00 D:252-348  [c       ode=2.30.42.10, no name defined]                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeee..-------.eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhh..--.eeeeee.-----------.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: D:254-326 UniProt: 254-326                                     --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2f0a D 251 mIITVTLNmEKYNFLGISIVGQ-------GIYIGSImKGGAVAADGRIEPGDmLLQVNDINFENmSNDDAVRVLRDIVHK--PIVLTVAK-----------LEHHHHHH 348
                            |      260       270 |     280      |290       300  |    310    |  320       330  |    340         - |       
                          251-MSE 259-MSE      272     280      |             303-MSE     315-MSE        330  |    340         341       
                                                              287-MSE                                       333                          

   Legend:   → Mismatch (orange background)
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    → 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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F0A)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DVL2_XENLA | P51142)
molecular function
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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:0045545    syndecan binding    Interacting selectively and non-covalently with syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0009948    anterior/posterior axis specification    The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0032053    ciliary basal body organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ciliary basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum).
    GO:0060026    convergent extension    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis.
    GO:0060027    convergent extension involved in gastrulation    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis usually resulting in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0009950    dorsal/ventral axis specification    The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0001736    establishment of planar polarity    Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
    GO:0007163    establishment or maintenance of cell polarity    Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
    GO:0007369    gastrulation    A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0001702    gastrulation with mouth forming second    A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0035253    ciliary rootlet    A cytoskeleton-like structure, originating from the basal body at the proximal end of a cilium, and extending proximally toward the cell nucleus. Rootlets are typically 80-100 nm in diameter and contain cross striae distributed at regular intervals of approximately 55-70 nm.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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