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(-) Description

Title :  STRUCTURES OF MITD1
 
Authors :  M. A. Hadders, M. Agromayor, A. Caballe, T. Obita, O. Perisic, R. L. Will J. Martin-Serrano
Date :  28 Oct 11  (Deposition) - 14 Nov 12  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein Transport, Escrt, Cytokinesis, Midbody (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Hadders, M. Agromayor, T. Obita, O. Perisic, A. Caballe, M. Kloc, M. H. Lamers, R. L. Williams, J. Martin-Serrano
Escrt-Iii Binding Protein Mitd1 Is Involved In Cytokinesis And Has An Unanticipated Pld Fold That Binds Membranes.
Proc. Natl. Acad. Sci. Usa V. 109 17424 2012
PubMed-ID: 23045692  |  Reference-DOI: 10.1073/PNAS.1206839109

(-) Compounds

Molecule 1 - MIT DOMAIN-CONTAINING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantC41
    Expression System VectorPOPTH
    Expression System Vector TypePLASMID
    FragmentMIT, RESIDUES 9-85
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITD1
 
Molecule 2 - CHARGED MULTIVESICULAR BODY PROTEIN 1A
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantC41
    Expression System VectorPOPTH
    Expression System Vector TypePLASMID
    FragmentRESIDUES 184-196
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHROMATIN-MODIFYING PROTEIN 1A, CHMP1A, VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 46-1, VPS46-1, HVPS46-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2P151Ligand/Ion2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2P15-1Ligand/Ion2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2P151Ligand/Ion2,5,8,11,14,17-HEXAOXANONADECAN-19-OL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:67 , TYR A:68BINDING SITE FOR RESIDUE GOL A1083
2AC2SOFTWAREASP B:26 , SER B:27 , TYR B:31 , TYR B:38 , LYS B:67 , ARG B:71 , ASN B:74 , TYR B:78 , HOH B:2015BINDING SITE FOR RESIDUE P15 B1082
3AC3SOFTWAREARG A:58 , HOH A:2016 , TYR B:78 , MET C:183 , GLU C:184 , ASP C:185BINDING SITE FOR RESIDUE GOL C1197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A5X)

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003979011ENSE00000946056chr16:89724129-89723990140CHM1A_HUMAN1-330--
1.2ENST000003979012ENSE00001530667chr16:89720331-8972031220CHM1A_HUMAN3-970--
1.3ENST000003979013ENSE00001778711chr16:89718054-8971797778CHM1A_HUMAN10-35260--
1.4ENST000003979014ENSE00001702069chr16:89715905-89715759147CHM1A_HUMAN36-84490--
1.5ENST000003979015ENSE00001784354chr16:89713739-89713611129CHM1A_HUMAN85-127430--
1.6ENST000003979016ENSE00001616577chr16:89713122-89712935188CHM1A_HUMAN128-190632C:183-190
D:181-190 (gaps)
8
25
1.7ENST000003979017ENSE00001798840chr16:89712495-897108461650CHM1A_HUMAN190-19672C:190-196
D:190-196
7
7

(-) 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:73
 aligned with MITD1_HUMAN | Q8WV92 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:73
                                    19        29        39        49        59        69        79   
          MITD1_HUMAN    10 PQSTAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTKDNTKRCNLREKISKYMDRAENIKKYLDQE  82
               SCOP domains d4a5xa_ A: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4a5x A  10 PQSTAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTKDNTKRCNLREKISKYMDRAENIKKYLDQE  82
                                    19        29        39        49        59        69        79   

Chain B from PDB  Type:PROTEIN  Length:73
 aligned with MITD1_HUMAN | Q8WV92 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:73
                                    18        28        38        48        58        68        78   
          MITD1_HUMAN     9 DPQSTAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTKDNTKRCNLREKISKYMDRAENIKKYLDQ  81
               SCOP domains d4a5xb_ B: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4a5x B   9 DPQSTAAATVLKRAVELDSESRYPQALVCYQEGIDLLLQVLKGTKDNTKRCNLREKISKYMDRAENIKKYLDQ  81
                                    18        28        38        48        58        68        78   

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with CHM1A_HUMAN | Q9HD42 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:14
                                   192    
          CHM1A_HUMAN   183 QEDQLSRRLAALRN 196
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
           Transcript 1 (1) Exon 1.6------ Transcript 1 (1)
           Transcript 1 (2) -------1.7     Transcript 1 (2)
                 4a5x C 183 MEDQLSRRLAALRN 196
                                   192    

Chain D from PDB  Type:PROTEIN  Length:16
 aligned with CHM1A_HUMAN | Q9HD42 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:31
                                   175       185       195 
          CHM1A_HUMAN   166 SQLPEGASAVGESSVRSQEDQLSRRLAALRN 196
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ..h---------------hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6 UniProt: 128-190------ Transcript 1 (1)
           Transcript 1 (2) ------------------------1.7     Transcript 1 (2)
                 4a5x D 181 SHM---------------EDQLSRRLAALRN 196
                              |      -       185       195 
                            183             184            

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A5X)

(-) Gene Ontology  (47, 58)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MITD1_HUMAN | Q8WV92)
molecular function
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0000920    cell separation after cytokinesis    The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    GO:0071985    multivesicular body sorting pathway    A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
cellular component
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.

Chain C,D   (CHM1A_HUMAN | Q9HD42)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:1904903    ESCRT III complex disassembly    The disaggregation of an ESCRT III complex into its constituent components.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0000920    cell separation after cytokinesis    The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
    GO:0016458    gene silencing    Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
    GO:0007076    mitotic chromosome condensation    The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
    GO:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    GO:0036258    multivesicular body assembly    The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0045014    negative regulation of transcription by glucose    Any process involving glucose that stops, prevents or reduces the rate of transcription. The presence of glucose in the growth medium inhibits the synthesis of certain enzymes in bacteria growing on the medium. For example, transcription of some catabolic operons is under negative control by specific repressors and glucose is an anti-inducer of xylose utilization and glycerol kinase.
    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:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010824    regulation of centrosome duplication    Any process that modulates the frequency, rate or extent of centrosome duplication. Centrosome duplication is the replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
    GO:1901673    regulation of mitotic spindle assembly    Any process that modulates the frequency, rate or extent of mitotic spindle assembly.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0007034    vacuolar transport    The directed movement of substances into, out of or within a vacuole.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
cellular component
    GO:0000815    ESCRT III complex    An endosomal sorting complex required for transport. Consists of two soluble subcomplexes of highly charged coiled-coil proteins and is required for sorting and/or concentration of multivesicular body (MVB) cargoes.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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
        CHM1A_HUMAN | Q9HD422jq9 2ymb
        MITD1_HUMAN | Q8WV922ymb 4a5z

(-) Related Entries Specified in the PDB File

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