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(-) Description

Title :  CRYSTAL STRUCTURE OF SET/TAF-1BETA/INHAT
 
Authors :  S. Muto, M. Senda, T. Senda, M. Horikoshi
Date :  18 Dec 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  P,Q  (1x)
Keywords :  Histone Chaperone, Inhat, Set, Pp2Ai, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Muto, M. Senda, Y. Akai, L. Sato, T. Suzuki, R. Nagai, T. Senda, M. Horikoshi
Relationship Between The Structure Of Set/Taf-Ibeta/Inhat And Its Histone Chaperone Activity
Proc. Natl. Acad. Sci. Usa V. 104 4285 2007
PubMed-ID: 17360516  |  Reference-DOI: 10.1073/PNAS.0603762104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN SET
    ChainsA, B, P, Q
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSET/TAF-1BETA(RESIDUES 1-225)
    GeneSET
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSET/TAF-1BETA, PHOSPHATASE 2A INHIBITOR I2PP2A, I-2PP2A, TEMPLATE-ACTIVATING FACTOR I, TAF-I, HLA-DR ASSOCIATED PROTEIN II, PHAPII, INHIBITOR OF GRANZYME A-ACTIVATED DNASE, IGAAD

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABPQ
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  PQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1TRE4Ligand/IonTREHALOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TRE2Ligand/IonTREHALOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1TRE2Ligand/IonTREHALOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , ASN A:61 , ARG A:64 , GLN A:65 , PHE A:68 , GLU A:114 , TRP A:213 , HOH A:228 , HOH A:229 , HOH A:237 , HOH A:241 , HOH A:243 , HOH A:244 , HOH A:246BINDING SITE FOR RESIDUE TRE A 226
2AC2SOFTWARESER A:2 , ALA A:5 , ALA A:6 , ASN A:46 , ALA A:49 , ILE A:53 , ARG B:64 , PHE B:68 , GLU B:114 , LYS B:209 , ASP B:210 , TRP B:213 , PRO B:214 , HOH B:229 , HOH B:242 , HOH B:249 , HOH B:250 , HOH B:256BINDING SITE FOR RESIDUE TRE B 226
3AC3SOFTWARELYS P:11 , ASN P:61 , ARG P:64 , GLN P:65 , PHE P:68 , GLU P:114 , TRP P:213 , HOH P:227 , HOH P:230 , HOH P:235 , HOH P:236 , HOH P:237 , HOH P:239BINDING SITE FOR RESIDUE TRE P 226
4AC4SOFTWARESER P:2 , ALA P:5 , ALA P:6 , ASN P:46 , ALA P:49 , SER P:50 , ILE P:53 , ARG Q:64 , PHE Q:68 , GLU Q:114 , LYS Q:209 , ASP Q:210 , TRP Q:213 , PRO Q:214 , HOH Q:237 , HOH Q:244 , HOH Q:248 , HOH Q:253BINDING SITE FOR RESIDUE TRE Q 226

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E50)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E50)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E50)

(-) Exons   (7, 28)

Asymmetric Unit (7, 28)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003726922aENSE00001696428chr9:131445934-131446286353SET_HUMAN1-38384A:1-25 (gaps)
B:24-25
P:1-25 (gaps)
Q:24-25
38
2
38
2
1.8bENST000003726928bENSE00000807004chr9:131453449-13145350658SET_HUMAN38-57204A:25-44
B:25-44
P:25-44
Q:25-44
20
20
20
20
1.9bENST000003726929bENSE00000807005chr9:131454137-131454279143SET_HUMAN57-105494A:44-92
B:44-92
P:44-92
Q:44-92
49
49
49
49
1.10cENST0000037269210cENSE00000807006chr9:131454941-131455044104SET_HUMAN105-139354A:92-126
B:92-126
P:92-126
Q:92-126
35
35
35
35
1.11cENST0000037269211cENSE00000807007chr9:131455147-131455260114SET_HUMAN140-177384A:127-164 (gaps)
B:127-164 (gaps)
P:127-164 (gaps)
Q:127-160 (gaps)
38
38
38
34
1.12ENST0000037269212ENSE00000807008chr9:131455917-131456087171SET_HUMAN178-234574A:165-221 (gaps)
B:165-221 (gaps)
P:165-221 (gaps)
Q:189-221 (gaps)
57
57
57
33
1.13bENST0000037269213bENSE00001052379chr9:131456175-131456321147SET_HUMAN235-283494A:222-222
B:222-223
P:222-222
Q:222-223
1
2
1
2
1.14fENST0000037269214fENSE00001894304chr9:131456920-1314586791760SET_HUMAN284-29070--

(-) 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:182
 aligned with SET_HUMAN | Q01105 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
            SET_HUMAN     1 MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLV 235
               SCOP domains d2  e50a1 A:1           -222      Protein SET                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh--hhhhhhhhh-----------hh..-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhh..eeeeeeee.......eeeeeee.........eeeeee.-------..ee...........----------------------hhhhhh------hhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-25 (gaps)         ------------------------------------------------------------------Exon 1.10c  PDB: A:92-126          Exon 1.11c  PDB: A:127-164 (gaps)     Exon 1.12  PDB: A:165-221 (gaps) UniProt: 178-234        1 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.8b           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) --------------------------------------------------------Exon 1.9b  PDB: A:44-92 UniProt: 57-105          ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2e50 A   1 MS--AQAAKVSKK-----------ELNS-----DETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFH-------SSKSTEIKWKSGKDM----------------------FFTWFT------ADELGEVIKDDIWPNPLQYYLV 222
                             |  |    8  |      -    |  | -   |    27        37        47        57        67        77        87        97       107       117       127       137      |  -    |  157        |-         -         - |    |  -   |   207       217     
                             2  3      11          12 15    21                                                                                                                        144     152           166                    189  194    201                     

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with SET_HUMAN | Q01105 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:200
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
            SET_HUMAN    37 GEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVP 236
               SCOP domains d2e50b_ B: Protein SET                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhh..eeeeeeee......eeeeeeee.........eeeeeee.------.eee...........----------------------hhhhhh-----.hhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.------------------------------------------------------------------Exon 1.10c  PDB: B:92-126          Exon 1.11c  PDB: B:127-164 (gaps)     Exon 1.12  PDB: B:165-221 (gaps) UniProt: 178-234        1. Transcript 1 (1)
           Transcript 1 (2) -Exon 1.8b           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) --------------------Exon 1.9b  PDB: B:44-92 UniProt: 57-105          ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2e50 B  24 SEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHM------SSKSTEIKWKSGKDM----------------------FFTWFT-----GADELGEVIKDDIWPNPLQYYLVP 223
                                    33        43        53        63        73        83        93       103       113       123       133       143 |     153       163  |      -         -     | 193|     |203       213       223
                                                                                                                                                   145    152           166                    189  194   200                       

Chain P from PDB  Type:PROTEIN  Length:186
 aligned with SET_HUMAN | Q01105 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
            SET_HUMAN     1 MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLV 235
               SCOP domains d2e50p_     P: Prote   in SE         T                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh----hhhhhh...---hhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh.eeeeeeee.......eeeeeee.........eeeeee.-------..ee............---------------------hhhhhh-----.hhhhhhhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: P:1-25 (gaps)         ------------------------------------------------------------------Exon 1.10c  PDB: P:92-126          Exon 1.11c  PDB: P:127-164 (gaps)     Exon 1.12  PDB: P:165-221 (gaps) UniProt: 178-234        1 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.8b           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) --------------------------------------------------------Exon 1.9b  PDB: P:44-92 UniProt: 57-105          ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2e50 P   1 MSAQAAK----VSKKELNSN---ADETS---------EKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFH-------SSKSTEIKWKSGKDMT---------------------FFTWFT-----GADELGEVIKDDIWPNPLQYYLV 222
                                  |  - |      16   |   | -       |27        37        47        57        67        77        87        97       107       117       127       137      |  -    |  157       167         -         - |    |  -  |    207       217     
                                  7    8      16  20  24        25                                                                                                                    144     152            167                   189  194   200                      

Chain Q from PDB  Type:PROTEIN  Length:159
 aligned with SET_HUMAN | Q01105 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:200
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
            SET_HUMAN    37 GEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVP 236
               SCOP domains d2e50q_ Q: Protein SET                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhh..eeeeeeee.......eeeeeee.........eeeeee.-------..ee.....----------------------------hhhhhh------hhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.------------------------------------------------------------------Exon 1.10c  PDB: Q:92-126          Exon 1.11c  PDB: Q:127-160 (gaps)     Exon 1.12  PDB: Q:189-221 (gaps) UniProt: 178-234        1. Transcript 1 (1)
           Transcript 1 (2) -Exon 1.8b           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) --------------------Exon 1.9b  PDB: Q:44-92 UniProt: 57-105          ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2e50 Q  24 SEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFH-------SSKSTEIKW----------------------------FFTWFT------ADELGEVIKDDIWPNPLQYYLVP 223
                                    33        43        53        63        73        83        93       103       113       123       133       143|      153      |  -         -         -     | 193|      203       213       223
                                                                                                                                                  144     152     160                          189  194    201                      

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E50)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,P,Q   (SET_HUMAN | Q01105)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0035067    negative regulation of histone acetylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0006337    nucleosome disassembly    The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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