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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOLIPASE C BETA 2
 
Authors :  S. N. Hicks, M. R. Jezyk, S. Gershberg, J. P. Seifert, T. K. Harden, J. Sondek
Date :  26 Mar 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  X
Keywords :  Phospholipase C, Phosphoinositide Phospholipase, Plc-Beta-2, Calcium, Coiled Coil, Hydrolase, Lipid Degradation, Metal- Binding, Transducer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. N. Hicks, M. R. Jezyk, S. Gershburg, J. P. Seifert, T. K. Harden, J. Sondek
General And Versatile Autoinhibition Of Plc Isozymes
Mol. Cell V. 31 383 2008
PubMed-ID: 18691970  |  Reference-DOI: 10.1016/J.MOLCEL.2008.06.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE BETA-2
    ChainsX
    EC Number3.1.4.11
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF21
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBACHT C
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES 1-799 (PH-C2 DOMAINS)
    GenePLC BETA 2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOINOSITIDE PHOSPHOLIPASE C, PHOSPHOLIPASE C- BETA-2, PLC-BETA-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN X:328 , GLU X:357 , ASP X:359 , GLU X:408 , HOH X:842 , HOH X:844BINDING SITE FOR RESIDUE CA X 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZKM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro X:365 -Pro X:366

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047509N324IPLCB2_HUMANPolymorphism45628633XN324I
2UniProtVAR_047510R598HPLCB2_HUMANPolymorphism8025153XR594H
3UniProtVAR_047511P664LPLCB2_HUMANPolymorphism9972332XP660L
4UniProtVAR_047512G712RPLCB2_HUMANPolymorphism28395835XG708R

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIPLC_X_DOMAINPS50007 Phosphatidylinositol-specific phospholipase X-box domain profile.PLCB2_HUMAN312-463  1X:312-463
2PIPLC_Y_DOMAINPS50008 Phosphatidylinositol-specific phospholipase Y-box domain profile.PLCB2_HUMAN546-662  1X:542-658
3C2PS50004 C2 domain profile.PLCB2_HUMAN669-767  1X:665-763

(-) Exons   (22, 22)

Asymmetric/Biological Unit (22, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002604021ENSE00002168435chr15:40600174-40599790385PLCB2_HUMAN1-28281X:11-2818
1.2ENST000002604022ENSE00001625850chr15:40596279-4059620278PLCB2_HUMAN29-54261X:29-5426
1.3ENST000002604023ENSE00001717589chr15:40595557-4059548969PLCB2_HUMAN55-77231X:55-7723
1.4ENST000002604024ENSE00001777308chr15:40594810-40594670141PLCB2_HUMAN78-124471X:78-12447
1.5ENST000002604025ENSE00001686556chr15:40594550-4059447180PLCB2_HUMAN125-151271X:125-15127
1.6ENST000002604026ENSE00001800063chr15:40594390-4059433754PLCB2_HUMAN151-169191X:151-16919
1.7ENST000002604027ENSE00001644083chr15:40594233-4059415876PLCB2_HUMAN169-194261X:169-19426
1.8ENST000002604028ENSE00001667829chr15:40591429-40591329101PLCB2_HUMAN195-228341X:195-22632
1.9ENST000002604029ENSE00001653269chr15:40591165-40590999167PLCB2_HUMAN228-284571X:235-277 (gaps)43
1.10ENST0000026040210ENSE00001728774chr15:40590909-40590763147PLCB2_HUMAN284-333501X:286-33348
1.11ENST0000026040211ENSE00001621090chr15:40590581-40590424158PLCB2_HUMAN333-385531X:333-38553
1.12ENST0000026040212ENSE00001795481chr15:40590160-4059007883PLCB2_HUMAN386-413281X:386-41328
1.13ENST0000026040213ENSE00001762039chr15:40589806-4058972285PLCB2_HUMAN413-441291X:413-44129
1.14bENST0000026040214bENSE00000883849chr15:40589109-40588947163PLCB2_HUMAN442-496551X:442-46524
1.15bENST0000026040215bENSE00000883848chr15:40588835-40588723113PLCB2_HUMAN496-533381X:516-52914
1.16ENST0000026040216ENSE00000883847chr15:40588593-4058849797PLCB2_HUMAN534-566331X:530-56233
1.17ENST0000026040217ENSE00000883846chr15:40587486-4058740285PLCB2_HUMAN566-594291X:562-59029
1.18ENST0000026040218ENSE00000883845chr15:40587261-40587137125PLCB2_HUMAN594-636431X:590-63243
1.19ENST0000026040219ENSE00001506972chr15:40586621-40586467155PLCB2_HUMAN636-687521X:632-68352
1.20ENST0000026040220ENSE00000883843chr15:40585925-40585761165PLCB2_HUMAN688-742551X:684-73855
1.21ENST0000026040221ENSE00000883842chr15:40585226-40585127100PLCB2_HUMAN743-776341X:739-77234
1.22ENST0000026040222ENSE00000883841chr15:40584644-40584540105PLCB2_HUMAN776-811361X:772-79928
1.23ENST0000026040223ENSE00000883840chr15:40584359-4058426595PLCB2_HUMAN811-842320--
1.24ENST0000026040224ENSE00000883839chr15:40584125-4058405076PLCB2_HUMAN843-868260--
1.25ENST0000026040225ENSE00000883838chr15:40583851-4058380745PLCB2_HUMAN868-883160--
1.26ENST0000026040226ENSE00000883837chr15:40583688-40583466223PLCB2_HUMAN883-957750--
1.27aENST0000026040227aENSE00000883836chr15:40583384-40583219166PLCB2_HUMAN957-1012560--
1.28ENST0000026040228ENSE00000883835chr15:40583038-4058296277PLCB2_HUMAN1013-1038260--
1.29ENST0000026040229ENSE00000883834chr15:40582873-4058277896PLCB2_HUMAN1038-1070330--
1.30ENST0000026040230ENSE00000883833chr15:40582283-4058222658PLCB2_HUMAN1070-1089200--
1.31ENST0000026040231ENSE00000883832chr15:40581559-4058147387PLCB2_HUMAN1090-1118290--
1.32ENST0000026040232ENSE00000883831chr15:40581119-405801001020PLCB2_HUMAN1119-1185670--

(-) 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 X from PDB  Type:PROTEIN  Length:708
 aligned with PLCB2_HUMAN | Q00722 from UniProtKB/Swiss-Prot  Length:1185

    Alignment length:793
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800   
          PLCB2_HUMAN    11 PKVKAYLSQGERFIKWDDETTVASPVILRVDPKGYYLYWTYQSKEMEFLDITSIRDTRFGKFAKMPKSQKLRDVFNMDFPDNSFLLKTLTVVSGPDMVDLTFHNFVSYKENVGKAWAEDVLALVKHPLTANASRSTFLDKILVKLKMQLNSEGKIPVKNFFQMFPADRKRVEAALSACHLPKGKNDAINPEDFPEPVYKSFLMSLCPRPEIDEIFTSYHAKAKPYMTKEHLTKFINQKQRDSRLNSLLFPPARPDQVQGLIDKYEPSGINAQRGQLSPEGMVWFLCGPENSVLAQDKLLLHHDMTQPLNHYFINSSHNTYLTAGQFSGLSSAEMYRQVLLSGCRCVELDCWKGKPPDEEPIITHGFTMTTDIFFKEAIEAIAESAFKTSPYPIILSFENHVDSPRQQAKMAEYCRTIFGDMLLTEPLEKFPLKPGVPLPSPEDLRGKILIKNKKNQFSGPTSSSKDTGGEAEGSSPPSAPAGEGTVWAGEEGTELEEEEVEEEEEEESGNLDEEEIKKMQSDEGTAGLEVTAYEEMSSLVNYIQPTKFVSFEFSAQKNRSYVISSFTELKAYDLLSKASVQFVDYNKRQMSRIYPKGTRMDSSNYMPQMFWNAGCQMVALNFQTMDLPMQQNMAVFEFNGQSGYLLKHEFMRRPDKQFNPFSVDRIDVVVATTLSITVISGQFLSERSVRTYVEVELFGLPGDPKRRYRTKLSPSTNSINPVWKEEPFVFEKILMPELASLRVAVMEEGNKFLGHRIIPINALNSGYHHLCLHSESNMPLTMPALFIFLEMKD 803
               SCOP domains d2zkmx3 X:11-141 Phospholipase C-beta-2                                                                                            d2zkmx1 X:142-311 Phospholipase C-beta-2                                                                                                                                  d2zkmx4 X:312-660 Phospholipase C-beta-2                                                                                                                                                                                                                                                                                                                         -----------------d2zkmx2 X:678-799 Phospholipase C-beta-2                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------efhand_        like-2zkmX02 X:2               20-311                                        --PI-PLC-X-2zkmX03 X:314-464                                                                                                                             -                                                      -------------------------PI-PLC-Y-2zkmX04 X:541-658                                                                                            ---------------------C2-2zkmX01 X:680-763                                                                ------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhheeeeee......eeeeeeee.....eeeeee....eeeee...eeeeee.hhh....hhhhhhhh.......hhhh.eeeeee.......eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......eehhhhhhhh..hhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhh.hhhhhh...--------..hhhhhhhhhhhh..---------------hhhhhhhhhh..--------.hhhhhhhhhhh......hhhhhh.......hhh.eee..................hhhhhhhhhh...eeeeeee.........ee.........eehhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhhhh.........................eeee....------------------------------------------------------..hhhhhhhhhhhhhhhhhh...hhhhhh.....ee....hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhheeeee............hhhhhhh...ee.......hhhhhhhhhhhhhhhhh.eee.hhhhh...................eeeeeeeeeee........eeeeeeee.........ee..................eeeeee.hhhh.eeeeeeee...eeeeeeeee.hhh..eeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H-----------------------------------------------------------------L-----------------------------------------------R------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PIPLC_X_DOMAIN  PDB: X:312-463 UniProt: 312-463                                                                                                         ----------------------------------------------------------------------------------PIPLC_Y_DOMAIN  PDB: X:542-658 UniProt: 546-662                                                                      ------C2  PDB: X:665-763 UniProt: 669-767                                                                ------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1          Exon 1.2  PDB: X:29-54    Exon 1.3  PDB: X:55-77 Exon 1.4  PDB: X:78-124 UniProt: 78-124        Exon 1.5  PDB: X:125-151   -----------------Exon 1.7  PDB: X:169-194  Exon 1.8  PDB: X:195-226          -------------------------------------------------------Exon 1.10  PDB: X:286-333 UniProt: 284-333        ----------------------------------------------------Exon 1.12  PDB: X:386-413   ----------------------------Exon 1.14b  PDB: X:442-465 UniProt: 442-496            -------------------------------------Exon 1.16  PDB: X:530-562        ---------------------------Exon 1.18  PDB: X:590-632 UniProt: 594-636 ---------------------------------------------------Exon 1.20  PDB: X:684-738 UniProt: 688-742             Exon 1.21  PDB: X:739-772         --------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6           ----------------------------------------------------------Exon 1.9  PDB: X:235-277 (gaps) UniProt: 228-284         ------------------------------------------------Exon 1.11  PDB: X:333-385 UniProt: 333-385           ---------------------------Exon 1.13  PDB: X:413-441    ------------------------------------------------------Exon 1.15b  PDB: X:516-529            --------------------------------Exon 1.17  PDB: X:562-590    -----------------------------------------Exon 1.19  PDB: X:632-683 UniProt: 636-687          ----------------------------------------------------------------------------------------Exon 1.22  PDB: X:772-799    Transcript 1 (2)
                 2zkm X  11 PKVKAYLSQGERFIKWDDETTVASPVILRVDPKGYYLYWTYQSKEMEFLDITSIRDTRFGKFAKMPKSQKLRDVFNMDFPDNSFLLKTLTVVSGPDMVDLTFHNFVSYKENVGKAWAEDVLALVKHPLTANASRSTFLDKILVKLKMQLNSEGKIPVKNFFQMFPADRKRVEAALSACHLPKGKNDAINPEDFPEPVYKSFLMSLCPRPEIDEIFT--------YMTKEHLTKFINQKQR---------------QVQGLIDKYEPS--------LSPEGMVWFLCGPENSVLAQDKLLLHHDMTQPLNHYFINSSHNTYLTAGQFSGLSSAEMYRQVLLSGCRCVELDCWKGKPPDEEPIITHGFTMTTDIFFKEAIEAIAESAFKTSPYPIILSFENHVDSPRQQAKMAEYCRTIFGDMLLTEPLEKFPLKPGVPLPSPEDLRGKILIKNKKN------------------------------------------------------NLDEEEIKKMQSDEGTAGLEVTAYEEMSSLVNYIQPTKFVSFEFSAQKNRSYVISSFTELKAYDLLSKASVQFVDYNKRQMSRIYPKGTRMDSSNYMPQMFWNAGCQMVALNFQTMDLPMQQNMAVFEFNGQSGYLLKHEFMRRPDKQFNPFSVDRIDVVVATTLSITVISGQFLSERSVRTYVEVELFGLPGDPKRRYRTKLSPSTNSINPVWKEEPFVFEKILMPELASLRVAVMEEGNKFLGHRIIPINALNSGYHHLCLHSESNMPLTMPALFIFLEMKD 799
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     |   -    |  240       250         -     | 270      |  -     | 290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460    |    -         -         -         -         -       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796   
                                                                                                                                                                                                                                                 226      235            250             266        277      286                                                                                                                                                                                465                                                    516                                                                                                                                                                                                                                                                                           

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZKM)

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: C2 (71)
(-)
Family: C2 (34)
(-)
Clan: EF_hand (270)
(-)
Clan: PLC (20)

(-) Gene Ontology  (19, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PLCB2_HUMAN | Q00722)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004435    phosphatidylinositol phospholipase C activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H(+).
    GO:0004629    phospholipase C activity    Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007223    Wnt signaling pathway, calcium modulating pathway    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC).
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    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:0006644    phospholipid metabolic process    The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0050913    sensory perception of bitter taste    The series of events required to receive a bitter taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLCB2_HUMAN | Q007222fju

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZKM)