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(-) Description

Title :  CRYSTAL STRUCTURE OF THE USP7:HDMX(AHSS) COMPLEX
 
Authors :  V. Saridakis
Date :  28 Apr 10  (Deposition) - 25 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Traf Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Sarkari, A. La Delfa, C. H. Arrowsmith, L. Frappier, Y. Sheng, V. Saridakis
Crystal Structure Of Usp7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
    ChainsA
    EC Number3.1.2.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePET15B
    FragmentUNP RESIDUES 54-205
    GeneHAUSP, USP7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainHUMAN
    SynonymUBIQUITIN THIOESTERASE 7, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 7, DEUBIQUITINATING ENZYME 7, HERPESVIRUS-ASSOCIATED UBIQUITIN-SPECIFIC PROTEASE
 
Molecule 2 - HDMX PEPTIDE
    ChainsB
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3MQR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MQR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.UBP7_HUMAN68-195  1A:68-195

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003448361ENSE00001413420chr16:9057341-9057064278UBP7_HUMAN1-27270--
1.3ENST000003448363ENSE00001363956chr16:9024254-9024150105UBP7_HUMAN27-62360--
1.4ENST000003448364ENSE00001368599chr16:9017270-9017072199UBP7_HUMAN62-128671A:63-128 (gaps)66
1.5ENST000003448365ENSE00001378973chr16:9015152-9015014139UBP7_HUMAN128-174471A:128-17447
1.6ENST000003448366ENSE00001384498chr16:9014304-901421689UBP7_HUMAN175-204301A:175-20430
1.7ENST000003448367ENSE00001364655chr16:9012996-9012888109UBP7_HUMAN204-240371A:204-2052
1.8ENST000003448368ENSE00001371018chr16:9011013-9010883131UBP7_HUMAN241-284440--
1.9ENST000003448369ENSE00001378062chr16:9010413-901035955UBP7_HUMAN284-302190--
1.10ENST0000034483610ENSE00001382791chr16:9009382-900930281UBP7_HUMAN303-329270--
1.11ENST0000034483611ENSE00001382051chr16:9009201-900911191UBP7_HUMAN330-360310--
1.12ENST0000034483612ENSE00001364905chr16:9004684-900460283UBP7_HUMAN360-387280--
1.13ENST0000034483613ENSE00001369206chr16:9002307-9002198110UBP7_HUMAN388-424370--
1.14ENST0000034483614ENSE00001370062chr16:9000439-9000283157UBP7_HUMAN424-476530--
1.15ENST0000034483615ENSE00001386233chr16:8999188-8999044145UBP7_HUMAN477-525490--
1.16ENST0000034483616ENSE00001369997chr16:8998422-8998292131UBP7_HUMAN525-568440--
1.17ENST0000034483617ENSE00001373075chr16:8997259-8997125135UBP7_HUMAN569-613450--
1.18ENST0000034483618ENSE00001385270chr16:8996339-8996238102UBP7_HUMAN614-647340--
1.19ENST0000034483619ENSE00001366300chr16:8996044-8995939106UBP7_HUMAN648-683360--
1.20ENST0000034483620ENSE00001403793chr16:8995091-899499993UBP7_HUMAN683-714320--
1.21ENST0000034483621ENSE00001416021chr16:8994914-899484768UBP7_HUMAN714-736230--
1.22ENST0000034483622ENSE00001413036chr16:8994487-8994387101UBP7_HUMAN737-770340--
1.23ENST0000034483623ENSE00001425600chr16:8993614-8993461154UBP7_HUMAN770-821520--
1.24ENST0000034483624ENSE00001432172chr16:8993045-899297868UBP7_HUMAN822-844230--
1.25ENST0000034483625ENSE00001431013chr16:8992496-8992388109UBP7_HUMAN844-880370--
1.26ENST0000034483626ENSE00001407007chr16:8992294-899221778UBP7_HUMAN881-906260--
1.27ENST0000034483627ENSE00001504725chr16:8990956-8990856101UBP7_HUMAN907-940340--
1.28ENST0000034483628ENSE00001504724chr16:8989598-8989499100UBP7_HUMAN940-973340--
1.29ENST0000034483629ENSE00001423657chr16:8989007-8988888120UBP7_HUMAN974-1013400--
1.30ENST0000034483630ENSE00001428927chr16:8988712-898864172UBP7_HUMAN1014-1037240--
1.31ENST0000034483631ENSE00001400057chr16:8988497-898840791UBP7_HUMAN1038-1068310--
1.32bENST0000034483632bENSE00001404180chr16:8987961-89859512011UBP7_HUMAN1068-1102350--

2.1aENST000003671821aENSE00001443738chr1:204485511-204485637127MDM4_HUMAN-00--
2.2aENST000003671822aENSE00002156140chr1:204494612-204494724113MDM4_HUMAN1-26260--
2.3ENST000003671823ENSE00001039934chr1:204495488-20449556275MDM4_HUMAN27-51250--
2.4ENST000003671824ENSE00001039926chr1:204499812-204499945134MDM4_HUMAN52-96450--
2.5aENST000003671825aENSE00001039924chr1:204501319-20450137456MDM4_HUMAN96-115200--
2.8aENST000003671828aENSE00001039927chr1:204506558-20450662568MDM4_HUMAN115-137230--
2.9dENST000003671829dENSE00001039922chr1:204507337-204507436100MDM4_HUMAN138-171340--
2.10bENST0000036718210bENSE00001075004chr1:204511912-204512072161MDM4_HUMAN171-224540--
2.11bENST0000036718211bENSE00001074998chr1:204513663-204513812150MDM4_HUMAN225-274500--
2.12bENST0000036718212bENSE00001075005chr1:204515925-20451600581MDM4_HUMAN275-301270--
2.13eENST0000036718213eENSE00001123001chr1:204518241-2045272489008MDM4_HUMAN302-4901891B:398-4014

(-) 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:137
 aligned with UBP7_HUMAN | Q93009 from UniProtKB/Swiss-Prot  Length:1102

    Alignment length:143
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202   
           UBP7_HUMAN    63 TSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGVAW 205
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhhhh...ee...eee..eeeeeeeeee.------..eeeeeeee.........eeeeeeeeee....hhhhheeeeeeeeee....eeeeeeeeehhhhh...........eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----MATH  PDB: A:68-195 UniProt: 68-195                                                                                             ---------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:63-128 (gaps) UniProt: 62-128 [INCOMPLETE]       ----------------------------------------------Exon 1.6  PDB: A:175-204      - Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.5  PDB: A:128-174 UniProt: 128-174      -----------------------------1. Transcript 1 (2)
                 3mqr A  63 TSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRF------QKSVGFFLQCNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGVAW 205
                                    72        82        92       102  |    112       122       132       142       152       162       172       182       192       202   
                                                                    105    112                                                                                             

Chain B from PDB  Type:PROTEIN  Length:4
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:4
           MDM4_HUMAN   398 AHSS 401
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
               Transcript 2 2.13 Transcript 2
                 3mqr B 398 AHSS 401

   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 3MQR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBP7_HUMAN | Q93009)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0010216    maintenance of DNA methylation    Any process involved in maintaining the methylation state of a nucleotide sequence.
    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:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051090    regulation of sequence-specific DNA binding transcription factor activity    Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:1904353    regulation of telomere capping    Any process that modulates the frequency, rate or extent of telomere capping.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
    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:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    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:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    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.

Chain B   (MDM4_HUMAN | O15151)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030330    DNA damage response, signal transduction by p53 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0045023    G0 to G1 transition    The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0071157    negative regulation of cell cycle arrest    Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDM4_HUMAN | O151512cr8 2mwy 2n06 2n0u 2n0w 2n14 2vje 2vjf 2vyr 3dab 3eqy 3fdo 3fe7 3fea 3jzo 3jzp 3jzq 3lbj 3u15 4rxz 5mnj
        UBP7_HUMAN | Q930091nb8 1nbf 1yy6 1yze 2f1w 2f1x 2f1y 2f1z 2foj 2foo 2fop 2kvr 2xxn 2ylm 3mqs 4jjq 4kg9 4m5w 4m5x 4pyz 4wph 4wpi 4yoc 4ysi 4z96 4z97 5c56 5c6d 5fwi 5gg4 5j7t 5jtj 5jtv

(-) Related Entries Specified in the PDB File

3mqs