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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH ERDJ5
 
Authors :  K. Inaba, M. Suzuki, K. Nagata
Date :  20 Oct 10  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdi Family, Thioredoxin, Endoplasmic Reticulum, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hagiwara, K. Maegawa, M. Suzuki, R. Ushioda, K. Araki, Y. Matsumoto J. Hoseki, K. Nagata, K. Inaba
Structural Basis Of An Erad Pathway Mediated By The Er-Resident Protein Disulfide Reductase Erdj5.
Mol. Cell V. 41 432 2011
PubMed-ID: 21329881  |  Reference-DOI: 10.1016/J.MOLCEL.2011.01.021

(-) Compounds

Molecule 1 - DNAJ HOMOLOG SUBFAMILY C MEMBER 10
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainORIGAMI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDNAJC10, ERDJ5, JPDI
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymER-RESIDENT PROTEIN ERDJ5, ENDOPLASMIC RETICULUM DNAJ-PDI FUSION PROTEIN 1, J DOMAIN-CONTAINING PROTEIN DISULFIDE ISOMERASE- LIKE PROTEIN, J DOMAIN-CONTAINING PDI-LIKE PROTEIN, JPDI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3APO)

(-) Sites  (0, 0)

(no "Site" information available for 3APO)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:186 -A:193
2A:294 -A:301
3A:403 -A:410
4A:508 -A:515
5A:616 -A:623
6A:728 -A:735

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:523 -Pro A:524
2Tyr A:631 -Pro A:632
3Tyr A:743 -Pro A:744

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 5)

Asymmetric/Biological Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.DJC10_MOUSE113-234
437-555
666-793
  3A:117-234
A:437-555
A:666-781
2THIOREDOXIN_1PS00194 Thioredoxin family active site.DJC10_MOUSE472-490
692-710
  2A:472-490
A:692-710

(-) Exons   (21, 21)

Asymmetric/Biological Unit (21, 21)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000283921ENSMUSE00000477397chr2:80155623-80155962340DJC10_MOUSE-00--
1.2ENSMUST000000283922ENSMUSE00000889499chr2:80157406-80157756351DJC10_MOUSE1-68681A:36-5722
1.3ENSMUST000000283923ENSMUSE00000165366chr2:80159317-80159479163DJC10_MOUSE69-123551A:81-123 (gaps)43
1.4ENSMUST000000283924ENSMUSE00000165373chr2:80161401-8016145151DJC10_MOUSE123-140181A:123-14018
1.5aENSMUST000000283925aENSMUSE00000403421chr2:80164817-8016489983DJC10_MOUSE140-167281A:140-16728
1.6ENSMUST000000283926ENSMUSE00000165376chr2:80165152-80165283132DJC10_MOUSE168-211441A:168-211 (gaps)44
1.7ENSMUST000000283927ENSMUSE00000165375chr2:80165775-8016586894DJC10_MOUSE212-243321A:212-24332
1.8ENSMUST000000283928ENSMUSE00000165370chr2:80166815-8016689278DJC10_MOUSE243-269271A:243-26927
1.9ENSMUST000000283929ENSMUSE00000240006chr2:80168229-8016827244DJC10_MOUSE269-283151A:269-28315
1.10aENSMUST0000002839210aENSMUSE00000239999chr2:80171426-80171563138DJC10_MOUSE284-329461A:284-329 (gaps)46
1.11aENSMUST0000002839211aENSMUSE00000165371chr2:80173086-8017317590DJC10_MOUSE330-359301A:330-35930
1.11dENSMUST0000002839211dENSMUSE00000165379chr2:80173883-80173996114DJC10_MOUSE360-397381A:360-397 (gaps)38
1.12ENSMUST0000002839212ENSMUSE00000165377chr2:80175610-80175724115DJC10_MOUSE398-436391A:398-43639
1.13ENSMUST0000002839213ENSMUSE00000165369chr2:80180630-80180757128DJC10_MOUSE436-478431A:436-47843
1.14bENSMUST0000002839214bENSMUSE00000239958chr2:80180969-80181085117DJC10_MOUSE479-517391A:479-51739
1.15ENSMUST0000002839215ENSMUSE00000239949chr2:80184074-80184175102DJC10_MOUSE518-551341A:518-55134
1.16ENSMUST0000002839216ENSMUSE00000428676chr2:80185081-80185236156DJC10_MOUSE552-603521A:552-60352
1.17ENSMUST0000002839217ENSMUSE00000239906chr2:80186669-80186802134DJC10_MOUSE604-648451A:604-64845
1.18ENSMUST0000002839218ENSMUSE00000239898chr2:80187501-8018755454DJC10_MOUSE648-666191A:648-66619
1.19aENSMUST0000002839219aENSMUSE00000239888chr2:80187805-80187952148DJC10_MOUSE666-715501A:666-71550
1.20ENSMUST0000002839220ENSMUSE00000239880chr2:80189426-80189545120DJC10_MOUSE716-755401A:716-75540
1.21aENSMUST0000002839221aENSMUSE00000413886chr2:80190786-80190890105DJC10_MOUSE756-790351A:756-78126
1.22ENSMUST0000002839222ENSMUSE00000688937chr2:80193016-801942001185DJC10_MOUSE791-79330--

(-) Sequences/Alignments

Asymmetric/Biological 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:688
 aligned with DJC10_MOUSE | Q9DC23 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:746
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775      
          DJC10_MOUSE    36 FYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKDEDLRKKYDKYGEKGLEDNQGGQYESWSYYRYDFGIYDDDPEIITLERREFDAAVNSGELWFVNFYSPGCSHCHDLAPTWREFAKEVDGLLRIGAVNCGDDRMLCRMKGVNSYPSLFIFRSGMAAVKYNGDRSKESLVAFAMQHVRSTVTELSTGNFVNAIETAFAAGVGWLITFCSKGEDCLTSQTRLRLSGMLDGLVNVGWVDCDAQDSLCKSLDTTASTTAYFPPGATLNDREKSSVLFLNSLDAKEIYMEIIHNLPDFELLSANQLEDRLAHHRWLVFFHFGKNENANDPELKKLKTLLKNEHIQVGRFDCSSAPGICSDLYVFQPCLAVFKGQGTKEYEIHHGKKILYDILAFAKESVNSHVTTLGPQNFPASDKEPWLVDFFAPWCPPCRALLPELRKASTLLYGQLKVGTLDCTIHEGLCNMYNIQAYPTTVVFNQSSIHEYEGHHSAEQILEFIEDLRNPSVVSLTPSTFNELVKQRKHDEVWMVDFYSPWCHPCQVLMPEWKRMARTLTGLINVGSVDCQQYHSFCTQENVQRYPEIRFYPQKSSKAYQYHSYNGWNRDAYSLRSWGLGFLPQASIDLTPQTFNEKVLQGKTHWVVDFYAPWCGPCQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLET 781
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....hhhhhhhhhh.-----------------------.hhhhhhhhhhhhhhhh..-----------------..............eee.hhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee........--------.eeeee......ee.....hhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh...eeeeeee...hhhhhh..-----.eeee.........hhhhheee...hhhhhhhhhhhhh....eehhhhhhhhhh..eeeeeee..-----.hhhhhhhhhhhh...eeeeeee...hhhhhhhh.....eeeeee......eee.....hhhhhhhhhhhhhh..eee.............eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhh........eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeee..........ee......hhhhhhhhhhh......eeehhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeeeee....eeeeeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------THIOREDOXIN_2  PDB: A:117-234 UniProt: 113-234                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: A:437-555 UniProt: 437-555                                                                         --------------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: A:666-781 UniProt: 666-793                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      ----------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:36-57           Exon 1.3  PDB: A:81-123 (gaps) UniProt: 69-123         ----------------Exon 1.5a  PDB: A:140-167   Exon 1.6  PDB: A:168-211 (gaps)             Exon 1.7  PDB: A:212-243        -------------------------Exon 1.9       Exon 1.10a  PDB: A:284-329 (gaps)             Exon 1.11a  PDB: A:330-359    Exon 1.11d  PDB: A:360-397 (gaps)     Exon 1.12  PDB: A:398-436              ------------------------------------------Exon 1.14b  PDB: A:479-517             Exon 1.15  PDB: A:518-551         Exon 1.16  PDB: A:552-603 UniProt: 552-603          Exon 1.17  PDB: A:604-648 UniProt: 604-648   -----------------Exon 1.19a  PDB: A:666-715 UniProt: 666-715       Exon 1.20  PDB: A:716-755               Exon 1.21a  PDB: A:756-781 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.4          ------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:243-269   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:436-478 UniProt: 436-478 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18          ------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3apo A  36 FYSLLGVSKTASSREIRQAFKK-----------------------NRAYEVLKDEDLRKKYDKY-----------------YYRYDFGIYDDDPEIITLERREFDAAVNSGELWFVNFYSPGSSHSHDLAPTWREFAKEVDGLLRIGAVNCGDDRMLC--------PSLFIFRSGMAAVKYNGDRSKESLVAFAMQHVRSTVTELSTGNFVNAIETAFAAGVGWLITFCSKGEDCLTSQTRLRLSGMLDGLVNVGWVDCDAQDSLCKSL-----TTAYFPPGATLNDREKSSVLFLNSLDAKEIYMEIIHNLPDFELLSANQLEDRLAHHRWLVFFHFG-----NDPELKKLKTLLKNEHIQVVRFDCSSAPGICSDLYVFQPSLAVFKGQGTKEYEIHHGKKILYDILAFAKESVNSHVTTLGPQNFPASDKEPWLVDFFAPWSPPSRALLPELRKASTLLYGQLKVGTLDCTIHEGLCNMYNIQAYPTTVVFNQSSIHEYEGHHSAEQILEFIEDLRNPSVVSLTPSTFNELVKQRKHDEVWMVDFYSPWSHPSQVLMPEWKRMARTLTGLINVGSVDCGQYHSFCTQENVQRYPEIRFYPQKSSKAYQYHSYNGWNRDAYSLRSWGLGFLPQASIDLTPQTFNEKVLQGKTHWVVDFYAPWSGPSQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLET 781
                                    45        55 |       -         -     |  85        95   |     -         - |     125       135       145       155       165       175       185       | -      |205       215       225       235       245       255       265       275       285       295        |-    |  315       325       335       345       355       365        |-    |  385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775      
                                                57                      81                99               117                                                                         193      202                                                                                                   304   310                                                             374   380                                                                                                                                                                                                                                                                                                                                                                                                                 

   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 3APO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DJC10_MOUSE | Q9DC23)
molecular function
    GO:0001671    ATPase activator activity    Binds to and increases the ATP hydrolysis activity of an ATPase.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    GO:0051787    misfolded protein binding    Interacting selectively and non-covalently with a misfolded protein.
    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:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    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:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:0034975    protein folding in endoplasmic reticulum    A protein folding process that takes place in the endoplasmic reticulum (ER). Secreted, plasma membrane and organelle proteins are folded in the ER, assisted by chaperones and foldases (protein disulphide isomerases), and additional factors required for optimal folding (ATP, Ca2+ and an oxidizing environment to allow disulfide bond formation).
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    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:0034663    endoplasmic reticulum chaperone complex    A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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    Tyr A:523 - Pro A:524   [ RasMol ]  
    Tyr A:631 - Pro A:632   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DJC10_MOUSE | Q9DC233apq 3aps 5ayk 5ayl

(-) Related Entries Specified in the PDB File

3apq 3aps