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(-) Description

Title :  C2 DOMAIN OF CYTOSOLIC PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  G. Y. Xu, T. Mcdonagh, H. A. Yu, E. A. Nalefski, J. D. Clark, D. A. Cumming
Date :  30 Apr 98  (Deposition) - 25 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Hydrolase, Lipid Degradation, Cytosolic Phospholipase A2, Calcium-Dependent Lipid Binding, C2 Domain, Phosphocholine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Y. Xu, T. Mcdonagh, H. A. Yu, E. A. Nalefski, J. D. Clark, D. A. Cumming
Solution Structure And Membrane Interactions Of The C2 Domain Of Cytosolic Phospholipase A2.
J. Mol. Biol. V. 280 485 1998
PubMed-ID: 9665851  |  Reference-DOI: 10.1006/JMBI.1998.1874
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOSOLIC PHOSPHOLIPASE A2
    Cell LinePROPRIETARY STRAIN/GI400
    ChainsA
    EC Number3.1.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LinePROPRIETARY STRAIN/GI400
    Expression System PlasmidPTRCHISB(INVITROGEN)
    Expression System Taxid562
    FragmentC2 DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALB DOMAIN

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:40 , THR A:41 , ASP A:43 , ASN A:64 , ASN A:65BINDING SITE FOR RESIDUE CA A 139
2AC2SOFTWAREASP A:43 , ASP A:93 , ALA A:94 , ASN A:95BINDING SITE FOR RESIDUE CA A 140

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029276G103RPA24A_HUMANPolymorphism28395828AG103R
2UniProtVAR_070778S111PPA24A_HUMANDisease121434634AS111P

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BCI)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003674661bENSE00001934855chr1:186798085-18679816783PA24A_HUMAN-00--
1.2aENST000003674662aENSE00002189438chr1:186823418-186823519102PA24A_HUMAN1-11110--
1.3ENST000003674663ENSE00000823084chr1:186839567-18683964882PA24A_HUMAN12-39281A:16-3924
1.5ENST000003674665ENSE00000790913chr1:186862143-186862291149PA24A_HUMAN39-88501A:39-8850
1.6ENST000003674666ENSE00000790914chr1:186863230-186863343114PA24A_HUMAN89-126381A:89-12638
1.7ENST000003674667ENSE00001002292chr1:186876097-18687613438PA24A_HUMAN127-139131A:127-13812
1.8ENST000003674668ENSE00000790915chr1:186880380-186880521142PA24A_HUMAN139-186480--
1.9ENST000003674669ENSE00000790916chr1:186901895-186902031137PA24A_HUMAN187-232460--
1.10ENST0000036746610ENSE00000790917chr1:186908140-186908362223PA24A_HUMAN232-306750--
1.11ENST0000036746611ENSE00000790918chr1:186909112-186909226115PA24A_HUMAN307-345390--
1.12ENST0000036746612ENSE00000790919chr1:186915769-186915906138PA24A_HUMAN345-391470--
1.13ENST0000036746613ENSE00000790920chr1:186916001-18691609393PA24A_HUMAN391-422320--
1.14ENST0000036746614ENSE00000790921chr1:186919789-18691986072PA24A_HUMAN422-446250--
1.15ENST0000036746615ENSE00000790922chr1:186925234-186925476243PA24A_HUMAN446-527820--
1.16ENST0000036746616ENSE00000790923chr1:186934541-186934725185PA24A_HUMAN527-588620--
1.17ENST0000036746617ENSE00000790924chr1:186946725-186946920196PA24A_HUMAN589-654660--
1.18ENST0000036746618ENSE00000790925chr1:186948447-186948604158PA24A_HUMAN654-706530--
1.19bENST0000036746619bENSE00001952949chr1:186957509-186958113605PA24A_HUMAN707-749430--

(-) Sequences/Alignments

NMR Structure
   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:123
 aligned with PA24A_HUMAN | P47712 from UniProtKB/Swiss-Prot  Length:749

    Alignment length:123
                                    25        35        45        55        65        75        85        95       105       115       125       135   
          PA24A_HUMAN    16 YSHKFTVVVLRATKVTKGAFGDMLDTPDPYVELFISTTPDSRKRTRHFNNDINPVWNETFEFILDPNQENVLEITLMDANYVMDETLGTATFTVSSMKVGEKKEVPFIFNQVTEMVLEMSLEV 138
               SCOP domains d1bcia_ A: Domain from cytosolic phospholipase A2                                                                           SCOP domains
               CATH domains 1bciA00 A:16-138 C2- domain Calcium/lipid binding domain                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee......hhhhh....eeeeee......eeeeeeee.....eeeeeeeeeee......eeeeeeeee....eeeeeeeeeee.....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------R-------P--------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:16-39  -------------------------------------------------Exon 1.6  PDB: A:89-126               Exon 1.7     Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.5  PDB: A:39-88 UniProt: 39-88             -------------------------------------------------- Transcript 1 (2)
                 1bci A  16 YSHKFTVVVLRATKVTKGAFGDMLDTPDPYVELFISTTPDSRKRTRHFNNDINPVWNETFEFILDPNQENVLEITLMDANYVMDETLGTATFTVSSMKVGEKKEVPFIFNQVTEMVLEMSLEV 138
                                    25        35        45        55        65        75        85        95       105       115       125       135   

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (63, 63)

NMR Structure(hide GO term definitions)
Chain A   (PA24A_HUMAN | P47712)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047498    calcium-dependent phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. This reaction requires Ca2+.
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    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:0004622    lysophospholipase activity    Catalysis of the reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008970    phosphatidylcholine 1-acylhydrolase activity    Catalysis of the reaction: phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a carboxylate.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
    GO:0004620    phospholipase activity    Catalysis of the hydrolysis of a glycerophospholipid.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0019369    arachidonic acid metabolic process    The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
    GO:0050482    arachidonic acid secretion    The controlled release of arachidonic acid from a cell or a tissue.
    GO:0035965    cardiolipin acyl-chain remodeling    Remodeling the acyl chains of premature (de novo synthesized) cardiolipin (1,3-bis(3-phosphatidyl)glycerol), through sequential deacylation and re-acylation reactions, to generate mature cardiolipin containing high-levels of unsaturated fatty acids.
    GO:0071236    cellular response to antibiotic    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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    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:0046456    icosanoid biosynthetic process    The chemical reactions and pathways resulting in the formation of icosanoids, any of a group of C20 polyunsaturated fatty acids.
    GO:0006690    icosanoid metabolic process    The chemical reactions and pathways involving icosanoids, any of a group of C20 polyunsaturated fatty acids.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0001554    luteolysis    The lysis or structural demise of the corpus luteum. During normal luteolysis, two closely related events occur. First, there is loss of the capacity to synthesize and secrete progesterone (functional luteolysis) followed by loss of the cells that comprise the corpus luteum (structural luteolysis). Preventing luteolysis is crucial to maintain pregnancy.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0001542    ovulation from ovarian follicle    The process leading to the rupture of the follicle, releasing the centrally located oocyte into the oviduct. An example of this is found in Mus musculus.
    GO:0006654    phosphatidic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0036151    phosphatidylcholine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.
    GO:0036152    phosphatidylethanolamine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylethanolamine, through sequential deacylation and re-acylation reactions, to generate phosphatidylethanolamine containing different types of fatty acid acyl chains.
    GO:0036148    phosphatidylglycerol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylglycerol, through sequential deacylation and re-acylation reactions, to generate phosphatidylglycerol containing different types of fatty acid acyl chains.
    GO:0036149    phosphatidylinositol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylinositol, through sequential deacylation and re-acylation reactions, to generate phosphatidylinositol containing different types of fatty acid acyl chains.
    GO:0036150    phosphatidylserine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylserine, through sequential deacylation and re-acylation reactions, to generate phosphatidylserine containing different types of fatty acid acyl chains.
    GO:0009395    phospholipid catabolic process    The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0006644    phospholipid metabolic process    The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0006663    platelet activating factor biosynthetic process    The chemical reactions and pathways resulting in the formation of platelet activating factor, 1-O-alkyl-2-acetyl-sn-glycerol 3-phosphocholine, where alkyl = hexadecyl or octadecyl. Platelet activating factor is an inflammatory mediator released from a variety of cells in response to various stimuli.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0030501    positive regulation of bone mineralization    Any process that activates or increases the frequency, rate or extent of bone mineralization.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0031622    positive regulation of fever generation    Any process that activates or increases the frequency, rate, or extent of fever generation.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0031394    positive regulation of prostaglandin biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of prostaglandin.
    GO:0031340    positive regulation of vesicle fusion    Any process that activates or increases the frequency, rate or extent of vesicle fusion.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0009408    response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0042542    response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0010226    response to lithium ion    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 lithium (Li+) ion stimulus.
    GO:0051597    response to methylmercury    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 methylmercury stimulus.
    GO:0010033    response to organic substance    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 an organic substance stimulus.
    GO:0010243    response to organonitrogen compound    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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0033280    response to vitamin D    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 vitamin D stimulus.
    GO:0043129    surfactant homeostasis    Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    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:0042588    zymogen granule    A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme.

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 Related Entries

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

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        PA24A_HUMAN | P477121cjy 1rlw

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