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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF THE 65KDA ISOFORM OF GLUTAMIC ACID DECARBOXYLASE (GAD65)
 
Authors :  A. M. Buckle, G. Fenalti, R. H. P. Law, J. C. Whisstock
Date :  17 Jan 07  (Deposition) - 27 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plp-Dependent Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Fenalti, R. H. Law, A. M. Buckle, C. Langendorf, K. Tuck, C. J. Rosado N. G. Faux, K. Mahmood, C. S. Hampe, J. P. Banga, M. Wilce, J. Schmidberger, J. Rossjohn, O. El-Kabbani, R. N. Pike, A. I. Smith, I. R. Mackay, M. J. Rowley, J. C. Whisstock
Gaba Production By Glutamic Acid Decarboxylase Is Regulated By A Dynamic Catalytic Loop.
Nat. Struct. Mol. Biol. V. 14 280 2007
PubMed-ID: 17384644  |  Reference-DOI: 10.1038/NSMB1228

(-) Compounds

Molecule 1 - GLUTAMATE DECARBOXYLASE 2
    ChainsA
    EC Number4.1.1.15
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidPRJ
    Expression System StrainYRD-15
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    FragmentRESIDUES 88-584
    GeneGAD2, GAD65
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLUTAMATE DECARBOXYLASE 65 KDA ISOFORM, GAD-65, 65 KDA GLUTAMIC ACID DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ABU2Ligand/IonGAMMA-AMINO-BUTANOIC ACID
2GOL1Ligand/IonGLYCEROL
3LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ABU4Ligand/IonGAMMA-AMINO-BUTANOIC ACID
2GOL2Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:181 , LEU A:182 , SER A:183 , PHE A:205 , THR A:339 , ARG A:558BINDING SITE FOR RESIDUE ABU A 585
2AC2SOFTWAREGLN A:181 , LEU A:182 , SER A:183 , ASN A:203 , HIS A:282 , LLP A:396 , CYS A:446 , HOH A:661BINDING SITE FOR RESIDUE ABU A 586
3AC3SOFTWAREGLU A:279 , SER A:281 , HIS A:282 , PHE A:283 , LYS A:286BINDING SITE FOR RESIDUE GOL A 587

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:98 -Pro A:99
2Asp A:438 -Thr A:439
3Gln A:583 -Asp A:584

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018822K124NDCE2_HUMANPolymorphism8190600AK124N
2UniProtVAR_029176P153QDCE2_HUMANPolymorphism2839672AP153Q
3UniProtVAR_029177G232EDCE2_HUMANPolymorphism2839673AG232E
4UniProtVAR_018823K286RDCE2_HUMANPolymorphism8190671AK286R
5UniProtVAR_029178G326ADCE2_HUMANPolymorphism2839678AG326A
6UniProtVAR_018824R375QDCE2_HUMANPolymorphism8190730AR375Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018822K124NDCE2_HUMANPolymorphism8190600AK124N
2UniProtVAR_029176P153QDCE2_HUMANPolymorphism2839672AP153Q
3UniProtVAR_029177G232EDCE2_HUMANPolymorphism2839673AG232E
4UniProtVAR_018823K286RDCE2_HUMANPolymorphism8190671AK286R
5UniProtVAR_029178G326ADCE2_HUMANPolymorphism2839678AG326A
6UniProtVAR_018824R375QDCE2_HUMANPolymorphism8190730AR375Q

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCE2_HUMAN389-410  1A:389-410
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DCE2_HUMAN389-410  2A:389-410

(-) Exons   (14, 14)

Asymmetric Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003762611aENSE00001470077chr10:26505236-26505814579DCE2_HUMAN1-26260--
1.2ENST000003762612ENSE00000926045chr10:26506539-2650659860DCE2_HUMAN26-46210--
1.3ENST000003762613ENSE00000926046chr10:26506771-26506920150DCE2_HUMAN46-96511A:88-969
1.5aENST000003762615aENSE00001675938chr10:26507972-26508205234DCE2_HUMAN96-174791A:96-17479
1.6ENST000003762616ENSE00001769139chr10:26512816-2651290691DCE2_HUMAN174-204311A:174-20431
1.7aENST000003762617aENSE00000638362chr10:26513468-26513580113DCE2_HUMAN204-242391A:204-24239
1.8ENST000003762618ENSE00000816175chr10:26518591-26518706116DCE2_HUMAN242-280391A:242-28039
1.9ENST000003762619ENSE00000926047chr10:26534850-2653492980DCE2_HUMAN281-307271A:281-30727
1.10ENST0000037626110ENSE00000926048chr10:26558048-2655810255DCE2_HUMAN307-325191A:307-32519
1.11ENST0000037626111ENSE00000926049chr10:26559569-26559685117DCE2_HUMAN326-364391A:326-36439
1.12ENST0000037626112ENSE00000926050chr10:26562565-2656262965DCE2_HUMAN365-386221A:365-38622
1.13ENST0000037626113ENSE00001787496chr10:26569938-2657001679DCE2_HUMAN386-412271A:386-41227
1.14ENST0000037626114ENSE00000816179chr10:26575274-26575423150DCE2_HUMAN413-462501A:413-462 (gaps)50
1.15ENST0000037626115ENSE00000816180chr10:26581394-26581501108DCE2_HUMAN463-498361A:463-49836
1.16ENST0000037626116ENSE00000816181chr10:26581831-2658192090DCE2_HUMAN499-528301A:499-528 (gaps)30
1.17bENST0000037626117bENSE00001738920chr10:26589717-265934873771DCE2_HUMAN529-585571A:529-58456

(-) 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:483
 aligned with DCE2_HUMAN | Q05329 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:497
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       
           DCE2_HUMAN    88 NYAFLHATDLLPACDGERPTLAFLQDVMNILLQYVVKSFDRSTKVIDFHYPNELLQEYNWELADQPQNLEEILMHCQTTLKYAIKTGHPRYFNQLSTGLDMVGLAADWLTSTANTNMFTYEIAPVFVLLEYVTLKKMREIIGWPGGSGDGIFSPGGAISNMYAMMIARFKMFPEVKEKGMAALPRLIAFTSEHSHFSLKKGAAALGIGTDSVILIKCDERGKMIPSDLERRILEAKQKGFVPFLVSATAGTTVYGAFDPLLAVADICKKYKIWMHVDAAWGGGLLMSRKHKWKLSGVERANSVTWNPHKMMGVPLQCSALLVREEGLMQNCNQMHASYLFQQDKHYDLSYDTGDKALQCGRHVDVFKLWLMWRAKGTTGFEAHVDKCLELAEYLYNIIKNREGYEMVFDGKPQHTNVCFWYIPPSLRTLEDNEERMSRLSKVAPVIKARMMEYGTTMVSYQPLGDKVNFFRMVISNPAATHQDIDFLIEEIERLGQD 584
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------Pyridoxal_deC-2okkA01 A:138-509                                                                                                                                                                                                                                                                                                                                                     --------   ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh.........hhhhhhhhhhhhhhhh.......ee.......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhhh.eeeeee.hhhhhhhh..hhhhhhhhhhh.eeee............eeeee...hhhhhhhh..-----------hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..........eeeee.........---.hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------N----------------------------Q------------------------------------------------------------------------------E-----------------------------------------------------R---------------------------------------A------------------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3 -----------------------------------------------------------------------------Exon 1.6  PDB: A:174-204       -------------------------------------Exon 1.8  PDB: A:242-280               --------------------------Exon 1.10          Exon 1.11  PDB: A:326-364              Exon 1.12             --------------------------Exon 1.14  PDB: A:413-462 (gaps) UniProt: 413-462 Exon 1.15  PDB: A:463-498           Exon 1.16 UniProt: 499-528    Exon 1.17b  PDB: A:529-584 UniProt: 529-585 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.5a  PDB: A:96-174 UniProt: 96-174                                       -----------------------------Exon 1.7a  PDB: A:204-242              --------------------------------------Exon 1.9  PDB: A:281-307   ------------------------------------------------------------------------------Exon 1.13  PDB: A:386-412  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2okk A  88 NYAFLHATDLLPACDGERPTLAFLQDVMNILLQYVVKSFDRSTKVIDFHYPNELLQEYNWELADQPQNLEEILMHCQTTLKYAIKTGHPRYFNQLSTGLDMVGLAADWLTSTANTNMFTYEIAPVFVLLEYVTLKKMREIIGWPGGSGDGIFSPGGAISNMYAMMIARFKMFPEVKEKGMAALPRLIAFTSEHSHFSLKKGAAALGIGTDSVILIKCDERGKMIPSDLERRILEAKQKGFVPFLVSATAGTTVYGAFDPLLAVADICKKYKIWMHVDAAWGGGLLMSRKHKWKLSGVERANSVTWNPHkMMGVPLQCSALLVREEGLMQNCNQMH-----------DLSYDTGDKALQCGRHVDVFKLWLMWRAKGTTGFEAHVDKCLELAEYLYNIIKNREGYEMVFDGKPQHTNVCFWYIPPSLRTLE---ERMSRLSKVAPVIKARMMEYGTTMVSYQPLGDKVNFFRMVISNPAATHQDIDFLIEEIERLGQD 584
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417    |    -      |437       447       457       467       477       487       497       507       517   |   527       537       547       557       567       577       
                                                                                                                                                                                                                                                                                                                                              396-LLP                   422         434                                                                                517 521                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2OKK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCE2_HUMAN | Q05329)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016595    glutamate binding    Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid.
    GO:0004351    glutamate decarboxylase activity    Catalysis of the reaction: L-glutamate = 4-aminobutanoate + CO2.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0006540    glutamate decarboxylation to succinate    The chemical reactions and pathways resulting in the formation of succinate from glutamate. Also known as GABA (gamma-aminobutyrate) shunt since it channels glutamate into the TCA cycle bypassing two steps of that cycle. There are three enzymes involved in the GABA shunt: glutamate decarboxylase (GAD), GABA aminotransferase (GABA-TA), and succinate semialdehyde dehydrogenase (SSADH). These three enzymes acting in concert to convert glutamate into succinate. The GABA shunt is predominantly associated with neurotransmission in the mammalian brain. It is also present in nonneuronal cells, in plants, in unicellular eukaryotes, and in prokaryotes.
    GO:0042136    neurotransmitter biosynthetic process    The chemical reactions and pathways resulting in the formation of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0061202    clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane    The lipid bilayer surrounding a clathrin-sculpted gamma-aminobutyric acid transport vesicle.
    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:0060077    inhibitory synapse    A synapse in which an action potential in the presynaptic cell reduces the probability of an action potential occurring in the postsynaptic cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.

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 Related Entries

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

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        DCE2_HUMAN | Q053291es0

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