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Title :  DR.MALLENA'S IN SILICO STRUCTURE GAP JUNCTION BETA-2 PROTEIN (CONNEXIN 26)
 
Authors :  S. C. Mallena, S. Mehanathan, A. Ramesh
Date :  22 Sep 04  (Deposition) - 12 Oct 04  (Release) - 26 Oct 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Deafness, Disease Mutation, Gap Junction, Polymorphism, Transmembrane, In Silico, Mallena (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Mallena, S. Mehanathan, A. Ramesh
Dr. Mallena'S In Silico Structure Of Gap Junction Beta-2 Protein (Connexin 26)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAP JUNCTION BETA-2 PROTEIN
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCONNEXIN 26, CX26

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XIR)

(-) Sites  (0, 0)

(no "Site" information available for 1XIR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XIR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (62, 62)

Theoretical Model (62, 62)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_015453G12RCXB2_HUMANDisease (KID syndrome)104894408AG12R
02UniProtVAR_015454S17FCXB2_HUMANDisease (KID syndrome)28929485AS17F
03UniProtVAR_002137V27ICXB2_HUMANPolymorphism2274084AV27I
04UniProtVAR_023605R32HCXB2_HUMANDisease (DFNB1A)111033190AR32H
05UniProtVAR_016839R32LCXB2_HUMANPolymorphism111033190AR32L
06UniProtVAR_002138M34TCXB2_HUMANUnclassified35887622AM34T
07UniProtVAR_002139V37ICXB2_HUMANDisease (DFNB1A)72474224AV37I
08UniProtVAR_008709W44CCXB2_HUMANDisease (DFNA3A)104894407AW44C
09UniProtVAR_032749W44SCXB2_HUMANDisease (DFNA3A)104894413AW44S
10UniProtVAR_015455G45ECXB2_HUMANPolymorphism72561723AG45E
11UniProtVAR_060798D46ECXB2_HUMANDisease (DFNA3A)  ---AD46E
12UniProtVAR_015456D50NCXB2_HUMANDisease (KID syndrome)28931594AD50N
13UniProtVAR_015935D50YCXB2_HUMANDisease (KID syndrome)28931594AD50Y
14UniProtVAR_032750N54KCXB2_HUMANDisease (BPS)104894412AN54K
15UniProtVAR_009965G59ACXB2_HUMANDisease (PPKDFN)104894404AG59A
16UniProtVAR_032751G59SCXB2_HUMANDisease (BPS)104894410AG59S
17UniProtVAR_008710D66HCXB2_HUMANDisease (VOWNKL)104894403AD66H
18UniProtVAR_015457I71TCXB2_HUMANUnclassified  ---AI71T
19UniProtVAR_060799H73RCXB2_HUMANDisease (PPKDFN)121912968AH73R
20UniProtVAR_015936R75QCXB2_HUMANDisease (PPKDFN)28931593AR75Q
21UniProtVAR_002140R75WCXB2_HUMANDisease (PPKDFN)104894402AR75W
22UniProtVAR_002141W77RCXB2_HUMANDisease (DFNB1A)104894397AW77R
23UniProtVAR_023607L79PCXB2_HUMANDisease (DFNB1A)  ---AL79P
24UniProtVAR_023608Q80KCXB2_HUMANDisease (DFNB1A)  ---AQ80K
25UniProtVAR_002142F83LCXB2_HUMANPolymorphism111033218AF83L
26UniProtVAR_002143V84LCXB2_HUMANDisease (DFNB1A)104894409AV84L
27UniProtVAR_060800V84MCXB2_HUMANDisease (DFNB1A)104894409AV84M
28UniProtVAR_015458T86RCXB2_HUMANDisease (DFNB1A)  ---AS86R
29UniProtVAR_015937L90PCXB2_HUMANDisease (DFNB1A)80338945AL90P
30UniProtVAR_023609M93ICXB2_HUMANDisease (DFNB1A)397516871AM93I
31UniProtVAR_002144V95MCXB2_HUMANDisease (DFNB1A)111033299AV95M
32UniProtVAR_015938I111TCXB2_HUMANPolymorphism  ---AI111T
33UniProtVAR_002145S113RCXB2_HUMANDisease (DFNB1A)80338946AS113R
34UniProtVAR_009966E114GCXB2_HUMANPolymorphism2274083AE114G
35UniProtVAR_069519D117HCXB2_HUMANPolymorphism  ---AD117H
36UniProtVAR_015459T123NCXB2_HUMANPolymorphism111033188AT123N
37UniProtVAR_015939R127HCXB2_HUMANPolymorphism111033196AR127H
38UniProtVAR_023611E129KCXB2_HUMANDisease (DFNB1A)397516875AE129K
39UniProtVAR_069520G130ACXB2_HUMANDisease (DFNB1A)  ---AG130A
40UniProtVAR_069521G130DCXB2_HUMANDisease (DFNB1A)779018464AG130D
41UniProtVAR_069522G130VCXB2_HUMANDisease (VOWNKL)  ---AG130V
42UniProtVAR_015940R143QCXB2_HUMANDisease (DFNA3A)104894401AR143Q
43UniProtVAR_015460R143WCXB2_HUMANDisease (DFNB1A)80338948AR143W
44UniProtVAR_069524A148PCXB2_HUMANPolymorphism  ---AA148P
45UniProtVAR_009967V153ICXB2_HUMANPolymorphism111033186AV153I
46UniProtVAR_015941D159VCXB2_HUMANDisease (DFNB1A)28931592AD159V
47UniProtVAR_002146G160SCXB2_HUMANPolymorphism34988750AG160S
48UniProtVAR_015942R165WCXB2_HUMANPolymorphism376898963AR165W
49UniProtVAR_023612V167MCXB2_HUMANPolymorphism111033360AV167M
50UniProtVAR_057959K168RCXB2_HUMANUnclassified200104362AK168R
51UniProtVAR_009968C169YCXB2_HUMANPolymorphism774518779AC169Y
52UniProtVAR_023613V178ACXB2_HUMANDisease (DFNB1A)568612627AV178A
53UniProtVAR_032752D179NCXB2_HUMANDisease (DFNA3A)28931595AD179N
54UniProtVAR_015943R184PCXB2_HUMANDisease (DFNB1A)80338950AR184P
55UniProtVAR_023614R184QCXB2_HUMANDisease (DFNA3A)80338950AR184Q
56UniProtVAR_009969R184WCXB2_HUMANDisease (DFNB1A)  ---AR184W
57UniProtVAR_015461F191LCXB2_HUMANPolymorphism397516878AF191L
58UniProtVAR_023615A197SCXB2_HUMANDisease (DFNA3A)  ---AA197S
59UniProtVAR_015944C202FCXB2_HUMANDisease (DFNA3A)104894406AC202F
60UniProtVAR_023616I203KCXB2_HUMANDisease (DFNB1A)  ---AI203K
61UniProtVAR_009970I203TCXB2_HUMANPolymorphism76838169AI203T
62UniProtVAR_023617L214PCXB2_HUMANDisease (DFNB1A)  ---AL214P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONNEXINS_1PS00407 Connexins signature 1.CXB2_HUMAN53-66  1A:53-66
2CONNEXINS_2PS00408 Connexins signature 2.CXB2_HUMAN169-185  1A:169-185

(-) Exons   (1, 1)

Theoretical Model (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003828481ENSE00001093399chr13:20767037-20766922116CXB2_HUMAN-00--
1.2bENST000003828482bENSE00001493557chr13:20763742-207616092134CXB2_HUMAN1-2342341A:1-226226

(-) Sequences/Alignments

Theoretical Model
   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:226
 aligned with CXB2_HUMAN | P29033 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           CXB2_HUMAN     1 MDWGTLQTILGGVNKHSTSIGKIWLTVLFIFRIMILVVAAKEVWGDEQADFVCNTLQPGCKNVCYDHYFPISHIRLWALQLIFVSTPALLVAMHVAYRRHEKKRKFIKGEIKSEFKDIEEIKTQKVRIEGSLWWTYTSSIFFRVIFEAAFMYVFYVMYDGFSMQRLVKCNAWPCPNTVDCFVSRPTEKTVFTVFMIAVSGICILLNVTELCYLLIRYCSGKSKKPV 226
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhh.....eeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...........ee...hhhhhhhh.....ee.........hhhhhhhhhhh...................................................... Sec.struct. author
             SAPs(SNPs) (1) -----------R----F---------I----H-T--I------CEE---N---K----A------H----T-R-Q-R-PK--LL-R---P--I-M---------------T-RG--H-----N---H-KA------------Q----P----I-----VS----W-MRY--------AN----P------L-----S----FK----------P------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------L-----------S-----Y--------S---------------W--------M---------------------------------------------D------------W----------------------------------------Q------------------T----------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------W------------------------------------------ SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------CONNEXINS_1   ------------------------------------------------------------------------------------------------------CONNEXINS_2      ----------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: A:1-226 UniProt: 1-234 [INCOMPLETE]                                                                                                                                                                                Transcript 1
                 1xir A   1 MDWGTLQTILGGVNKHSTSIGKIWLTVLFIFRIMILVVAAKEVWGDEQADFVCNTLQPGCKNVCYDHYFPISHIRLWALQLIFVSSPALLVAMHVAYRRHEKKRKFIKGEIKSEFKDIEEIKTQKVRIEGSLWWTYTSSIFFRVIFEAAFMYVFYVMYDGFSMQRLVKCNAWPCPNTVDCFVSRPTEKTVFTVFMIAVSGICILLNVTELCYLLIRYCSGKSKKPV 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      

   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 1XIR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XIR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XIR)

(-) Gene Ontology  (23, 23)

Theoretical Model(hide GO term definitions)
Chain A   (CXB2_HUMAN | P29033)
molecular function
    GO:0005243    gap junction channel activity    A wide pore channel activity that enables a direct cytoplasmic connection from one cell to an adjacent cell. The gap junction can pass large solutes as well as electrical signals between cells. Gap junctions consist of two gap junction hemi-channels, or connexons, one contributed by each membrane through which the gap junction passes.
biological process
    GO:0007154    cell communication    Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0034599    cellular response to oxidative 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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0046697    decidualization    The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0016264    gap junction assembly    Assembly of gap junctions, which are found in most animal tissues, and serve as direct connections between the cytoplasms of adjacent cells. They provide open channels through the plasma membrane, allowing ions and small molecules (less than approximately a thousand daltons) to diffuse freely between neighboring cells, but preventing the passage of proteins and nucleic acids.
    GO:0030539    male genitalia development    The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0044752    response to human chorionic gonadotropin    Any process that results in a change in state or activity of a cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a human chorionic gonadotropin stimulus.
    GO:0032570    response to progesterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005922    connexin complex    An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0005921    gap junction    A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CXB2_HUMAN | P290332zw3 3iz1 3iz2 5er7 5era 5kj3 5kjg

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