Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PHF2 JUMONJI-NOG-FE(II) COMPLEX
 
Authors :  J. R. Horton, A. K. Upadhyay, H. Hashimoto, X. Zhang, X. Cheng
Date :  03 Dec 10  (Deposition) - 26 Jan 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Alpha-Ketoglutarate-Fe2+ Dependent Dioxygenases, Histone Tail Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, A. K. Upadhyay, H. Hashimoto, X. Zhang, X. Cheng
Structural Basis For Human Phf2 Jumonji Domain Interaction With Metal Ions.
J. Mol. Biol. V. 406 1 2011
PubMed-ID: 21167174  |  Reference-DOI: 10.1016/J.JMB.2010.12.013

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 2
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC870
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: JUMONJI DOMAIN (UNP RESIDUES 60-451)
    Gene: PHF2, KIAA0662
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GRC5

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric Unit (6, 30)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO18Ligand/Ion1,2-ETHANEDIOL
3FE2Ligand/IonFE (III) ION
4OGA2Ligand/IonN-OXALYLGLYCINE
5OXY2Ligand/IonOXYGEN MOLECULE
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FE-1Ligand/IonFE (III) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5OXY1Ligand/IonOXYGEN MOLECULE
6SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3FE-1Ligand/IonFE (III) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5OXY1Ligand/IonOXYGEN MOLECULE
6SO42Ligand/IonSULFATE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREOGA A:2 , HOH A:58 , THR A:193 , HIS A:335BINDING SITE FOR RESIDUE OXY A 1
02AC2SOFTWAREOGA B:1 , HOH B:31 , THR B:193 , HIS B:335BINDING SITE FOR RESIDUE OXY B 2
03AC3SOFTWAREHOH A:17 , SER A:198 , LYS A:232 , THR A:234 , HOH A:493 , HOH A:551BINDING SITE FOR RESIDUE EDO A 452
04AC4SOFTWAREPHE B:89 , ARG B:96 , PHE B:294 , HOH B:546BINDING SITE FOR RESIDUE EDO B 452
05AC5SOFTWAREPHE B:426 , LYS B:427 , HOH B:528BINDING SITE FOR RESIDUE EDO B 4
06AC6SOFTWAREHOH B:52 , LYS B:230 , HOH B:539 , HOH B:604BINDING SITE FOR RESIDUE EDO B 5
07AC7SOFTWARELEU B:115 , GLY B:116 , LYS B:214 , HOH B:561BINDING SITE FOR RESIDUE EDO B 6
08AC8SOFTWAREARG A:272 , HOH A:515 , ALA B:416 , ASP B:420BINDING SITE FOR RESIDUE EDO A 7
09AC9SOFTWAREPHE A:426 , LYS A:427BINDING SITE FOR RESIDUE EDO A 8
10BC1SOFTWARELYS A:175 , ASP A:179 , LYS B:131BINDING SITE FOR RESIDUE EDO A 9
11BC2SOFTWAREGLU A:219 , ASN A:220 , HOH A:519BINDING SITE FOR RESIDUE EDO A 10
12BC3SOFTWARELYS A:214 , LEU A:215 , TYR A:221 , HIS A:338 , SER A:339BINDING SITE FOR RESIDUE EDO A 11
13BC4SOFTWAREGLU A:92 , LEU A:93BINDING SITE FOR RESIDUE EDO A 12
14BC5SOFTWAREEDO A:14 , SER A:317 , LEU A:340 , SER A:341 , MET A:344 , HOH A:515BINDING SITE FOR RESIDUE EDO A 13
15BC6SOFTWAREEDO A:13 , EDO A:15 , LEU A:340 , SER A:341 , VAL A:342 , GLU A:343 , MET A:344 , HOH A:520BINDING SITE FOR RESIDUE EDO A 14
16BC7SOFTWAREEDO A:14 , SER A:339 , LEU A:340 , SER A:341 , VAL A:342 , HIS A:394 , GLY A:398 , ILE A:401BINDING SITE FOR RESIDUE EDO A 15
17BC8SOFTWAREARG A:186 , VAL A:241 , LYS A:242BINDING SITE FOR RESIDUE EDO A 16
18BC9SOFTWAREMET B:346 , TYR B:349 , GLU B:350 , ARG B:353 , TRP B:409BINDING SITE FOR RESIDUE EDO B 17
19CC1SOFTWAREASP A:179 , TYR A:182BINDING SITE FOR RESIDUE EDO A 18
20CC2SOFTWAREGLU B:119 , LEU B:215 , HIS B:394BINDING SITE FOR RESIDUE EDO B 20
21CC3SOFTWAREOXY B:2 , HOH B:31 , HOH B:54 , LEU B:238 , HIS B:249 , ASP B:251 , TYR B:259 , LYS B:266 , TYR B:321 , THR B:323 , HIS B:335 , FE B:454BINDING SITE FOR RESIDUE OGA B 1
22CC4SOFTWAREOXY A:1 , HOH A:58 , LEU A:238 , THR A:246 , HIS A:249 , ASP A:251 , TYR A:259 , LYS A:266 , TYR A:321 , THR A:323 , HIS A:335 , FE A:453 , HOH A:481BINDING SITE FOR RESIDUE OGA A 2
23CC5SOFTWARESER B:216 , TRP B:217 , VAL B:218 , LEU B:337 , HOH B:588BINDING SITE FOR RESIDUE CL B 453
24CC6SOFTWARESER A:216 , TRP A:217 , VAL A:218 , PHE A:336 , LEU A:337 , HOH A:498BINDING SITE FOR RESIDUE CL A 4
25CC7SOFTWAREOGA B:1 , HIS B:249 , ASP B:251 , TYR B:321 , HOH B:545BINDING SITE FOR RESIDUE FE B 454
26CC8SOFTWAREOGA A:2 , HIS A:249 , ASP A:251 , TYR A:321 , HOH A:475BINDING SITE FOR RESIDUE FE A 453
27CC9SOFTWAREASP A:133 , GLY A:134 , LEU A:135 , GLY A:136 , HOH A:469BINDING SITE FOR RESIDUE SO4 A 454
28DC1SOFTWARESER A:275 , ILE A:278 , MET A:344 , ARG A:347BINDING SITE FOR RESIDUE SO4 A 455
29DC2SOFTWAREASP B:133 , GLY B:134 , LEU B:135 , GLY B:136 , HOH B:473BINDING SITE FOR RESIDUE SO4 B 12
30DC3SOFTWARELYS A:304 , TYR B:152 , ARG B:201BINDING SITE FOR RESIDUE SO4 B 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PU8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:184 -Asn A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PU8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  2A:197-353
B:197-353
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  1-
B:197-353
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  1A:197-353
-

(-) Exons   (0, 0)

(no "Exon" information available for 3PU8)

(-) 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:363
 aligned with PHF2_HUMAN | O75151 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:363
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442   
           PHF2_HUMAN    83 QNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENA 445
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhh.ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhh.......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeee..eeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhh...eeeee....eeee....eeeeee...eeeeeeee....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:197-353 UniProt: 197-353                                                                                                                        -------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pu8 A  83 QNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENA 445
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442   


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with PHF2_HUMAN | O75151 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:365
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     
           PHF2_HUMAN    80 KPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSEN 444
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3pu8B01 B:236-336                                                                               ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3pu8B02 B:236-336                                                                               ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhh...hhhhh.ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhh.......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee...eeee....eeeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:197-353 UniProt: 197-353                                                                                                                        ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pu8 B  80 KPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSEN 444
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439
   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 3PU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PU8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Family: JmjC (39)
(-)
Homo sapiens (Human) (31)
1aJmjC-3pu8B01B:236-336
1bJmjC-3pu8B02B:236-336

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHF2_HUMAN | O75151)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0032454    histone demethylase activity (H3-K9 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0033169    histone H3-K9 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0061188    negative regulation of chromatin silencing at rDNA    Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006482    protein demethylation    The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:184 - Asn A:185   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  3pu8
    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
  PHF2_HUMAN | O75151
    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
  PHF2_HUMAN | O75151
    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
        PHF2_HUMAN | O75151: 3kqi 3ptr 3pu3 3pua 3pus

(-) Related Entries Specified in the PDB File

3ptr PHF2 JUMONJI DOMAIN
3pu3 PHF2 JUMONJI-NOG
3pua
3pus