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(-) Description

Title :  STRUCTURE OF HUMAN CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA (CAMK2A) IN COMPLEX WITH INDIRUBIN E804
 
Authors :  A. C. W. Pike, P. Rellos, O. King, E. Salah, E. Parizotto, O. Fedorov, L. S N. Burgess-Brown, A. Roos, J. W. Murray, F. Von Delft, A. Edwards, C. H. Arrowsmith, M. Wikstroem, C. Bountra, S. Knapp
Date :  30 Jul 08  (Deposition) - 26 Aug 08  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Serine/Threonine-Protein Kinase, Atp-Binding, Cell Junction, Cell Membrane, Long Term Potentiation, Brain, Kinase, Synapse, Membrane, Nmda Receptor Signalling, Phosphoprotein, Calmodulin-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Rellos, A. C. W. Pike, F. H. Niesen, E. Salah, W. H. Lee, F. Von Delft, S. Knapp
Structure Of The Camkiidelta/Calmodulin Complex Reveals The Molecular Mechanism Of Camkii Kinase Activation.
Plos Biol. V. 8 426 2010
PubMed-ID: 20668654  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000426

(-) Compounds

Molecule 1 - CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
    ChainsA, B
    EC Number2.7.11.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentKINASE DOMAIN, RESIDUES 13-302
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCAM-KINASE II ALPHA CHAIN, CAM KINASE II SUBUNIT ALPHA, CAMK-II SUBUNIT ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FEF2Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}
2PGO3Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FEF1Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}
2PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FEF1Ligand/Ion(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}
2PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:19 , ALA A:40 , PHE A:89 , ASP A:90 , LEU A:91 , VAL A:92 , GLU A:139 , ASN A:140 , LEU A:142 , ASP A:156BINDING SITE FOR RESIDUE FEF A 600
2AC2SOFTWARELEU B:19 , ALA B:40 , PHE B:89 , ASP B:90 , LEU B:91 , VAL B:92 , GLU B:139 , LEU B:142 , ASP B:156BINDING SITE FOR RESIDUE FEF B 600
3AC3SOFTWAREGLN A:117 , ILE A:271 , HIS A:273 , ARG A:274 , SER A:275 , PGO A:1302 , HOH A:2146 , SER B:108 , ALA B:110 , ASP B:111BINDING SITE FOR RESIDUE PGO A1301
4AC4SOFTWAREARG A:274 , SER A:275 , PGO A:1301 , HOH A:2147 , CYS B:280BINDING SITE FOR RESIDUE PGO A1302
5AC5SOFTWAREARG A:52 , GLN A:55 , GLU B:236 , GLU B:285 , CYS B:289 , HOH B:2111BINDING SITE FOR RESIDUE PGO B1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VZ6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:234 -Pro A:235
2Ser B:234 -Pro B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VZ6)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KCC2A_HUMAN19-42
 
  2A:19-42
B:19-42
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KCC2A_HUMAN131-143
 
  2A:131-143
B:131-143
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KCC2A_HUMAN19-42
 
  1A:19-42
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KCC2A_HUMAN131-143
 
  1A:131-143
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KCC2A_HUMAN19-42
 
  1-
B:19-42
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KCC2A_HUMAN131-143
 
  1-
B:131-143

(-) Exons   (0, 0)

(no "Exon" information available for 2VZ6)

(-) 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:291
 aligned with KCC2A_HUMAN | Q9UQM7 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:293
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296   
          KCC2A_HUMAN     7 TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKL 299
               SCOP domains d2vz6a_ A: auto  mated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------2vz6A02 A:92-299 Transferase(Phosphotransferase) domain 1                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeee.--..eeeeeee.hhheeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee........eee......ee.............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vz6 A  -5 LYFQSMYQLFEELGK--FSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKL 299
                                 || 16    |  |26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296   
                                 0|      21 24                                                                                                                                                                                                                                                                                   
                                 13                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with KCC2A_HUMAN | Q9UQM7 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:294
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
          KCC2A_HUMAN     7 TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKLK 300
               SCOP domains d2vz6b_ B: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------2vz6B02 B:92-300 Transferase(Phosphotransferase) domain 1                                                                                                                                                         CATH domains
           Pfam domains (1) ------Pkinase-2vz6B01 B:13-271                                                                                                                                                                                                                                           ----------------------------- Pfam domains (1)
           Pfam domains (2) ------Pkinase-2vz6B02 B:13-271                                                                                                                                                                                                                                           ----------------------------- Pfam domains (2)
         Sec.struct. author .hhhhheeeeeeeee...eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee........eee......ee.............hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vz6 B  -5 LYFQSMYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKLK 300
                                 || 16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
                                 0|                                                                                                                                                                                                                                                                                               
                                 13                                                                                                                                                                                                                                                                                               

   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  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KCC2A_HUMAN | Q9UQM7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    GO:0035254    glutamate receptor binding    Interacting selectively and non-covalently with a glutamate receptor.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    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:0038166    angiotensin-activated signaling pathway    The series of molecular signals generated as a consequence of angiotensin II binding to an angiotensin receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0051928    positive regulation of calcium ion transport    Any process that activates or increases the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010666    positive regulation of cardiac muscle cell apoptotic process    Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:1902108    regulation of mitochondrial membrane permeability involved in apoptotic process    Any regulation of mitochondrial membrane permeability that is involved in apoptotic process.
    GO:0048168    regulation of neuronal synaptic plasticity    A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0046928    regulation of neurotransmitter secretion    Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell.
    GO:0002931    response to ischemia    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 inadequate blood supply.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.
    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.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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        KCC2A_HUMAN | Q9UQM73soa 5ig3

(-) Related Entries Specified in the PDB File

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