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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3RD PDZ DOMAIN OF HUMAN DISCS LARGE HOMOLOGUE 2, DLG2
 
Authors :  A. P. Turnbull, C. Phillips, G. Berridge, P. Savitsky, C. E. A. Smee, E. Papagrigoriou, J. Debreczeni, F. Gorrec, J. M. Elkins, F. Von Delft, J. Weigelt, A. Edwards, C. Arrowsmith, M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)
Date :  21 Jun 06  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dlg2, Pdz, Pdz Domain, Signal Transduction, Structural Genomics, Structural Genomics Consortium, Sgc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Elkins, E. Papagrigoriou, G. Berridge, X. Yang, C. Phillips, C. Gileadi, P. Savitsky, D. A. Doyle
Structure Of Pick1 And Other Pdz Domains Obtained With The Help Of Self-Binding C-Terminal Extensions.
Protein Sci. V. 16 683 2007
PubMed-ID: 17384233  |  Reference-DOI: 10.1110/PS.062657507
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DISCS LARGE HOMOLOG 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3/ROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDLG2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOSTSYNAPTIC DENSITY PROTEIN PSD-93, CHANNEL- ASSOCIATED PROTEIN OF SYNAPSE-110, CHAPSYN-110

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2HE2)

(-) Sites  (0, 0)

(no "Site" information available for 2HE2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HE2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HE2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HE2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG2_HUMAN98-185
193-280
421-502
 
  2-
-
A:421-502
B:421-502
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG2_HUMAN98-185
193-280
421-502
 
  1-
-
A:421-502
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG2_HUMAN98-185
193-280
421-502
 
  1-
-
-
B:421-502

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.11aENST0000039830911aENSE00002179742chr11:84634633-84634121513DLG2_HUMAN1-14140--
1.13bENST0000039830913bENSE00001303881chr11:84245774-84245613162DLG2_HUMAN15-68540--
1.18ENST0000039830918ENSE00001788484chr11:83962334-8396228154DLG2_HUMAN69-86180--
1.20ENST0000039830920ENSE00001641623chr11:83874554-8387450451DLG2_HUMAN87-103170--
1.21bENST0000039830921bENSE00001784581chr11:83810090-83809966125DLG2_HUMAN104-145420--
1.22bENST0000039830922bENSE00001618276chr11:83770527-83770358170DLG2_HUMAN145-202580--
1.23bENST0000039830923bENSE00001707546chr11:83691685-83691549137DLG2_HUMAN202-247460--
1.24ENST0000039830924ENSE00001665304chr11:83676511-83676367145DLG2_HUMAN248-296490--
1.25bENST0000039830925bENSE00001660049chr11:83674066-83673928139DLG2_HUMAN296-342470--
1.26ENST0000039830926ENSE00001688351chr11:83641526-83641371156DLG2_HUMAN342-394530--
1.27ENST0000039830927ENSE00001745803chr11:83585531-8358546369DLG2_HUMAN394-417242A:-1-418
B:0-0
3
1
1.28ENST0000039830928ENSE00001790848chr11:83544813-83544657157DLG2_HUMAN417-469532A:419-469
B:0-469
51
53
1.29aENST0000039830929aENSE00001620072chr11:83497835-83497733103DLG2_HUMAN470-504352A:470-504
B:470-504
35
35
1.35aENST0000039830935aENSE00001781764chr11:83344368-83344254115DLG2_HUMAN504-542392A:504-517 (gaps)
B:504-517 (gaps)
21
21
1.36bENST0000039830936bENSE00001157212chr11:83252901-83252725177DLG2_HUMAN542-601600--
1.37bENST0000039830937bENSE00002198764chr11:83243826-8324375176DLG2_HUMAN601-626260--
1.39aENST0000039830939aENSE00001157190chr11:83195271-83195172100DLG2_HUMAN627-660340--
1.42aENST0000039830942aENSE00001775400chr11:83183820-8318377051DLG2_HUMAN660-677180--
1.43ENST0000039830943ENSE00002198604chr11:83182770-83182669102DLG2_HUMAN677-711350--
1.44bENST0000039830944bENSE00001749092chr11:83180416-83180244173DLG2_HUMAN711-768580--
1.45ENST0000039830945ENSE00001664999chr11:83177860-83177751110DLG2_HUMAN769-805370--
1.46cENST0000039830946cENSE00001680261chr11:83173136-8317304592DLG2_HUMAN805-836320--
1.47iENST0000039830947iENSE00001291156chr11:83170967-831660554913DLG2_HUMAN836-870350--

(-) 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:102
 aligned with DLG2_HUMAN | Q15700 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:111
                                   423       433       443       453       463       473       483       493       503       513       523 
           DLG2_HUMAN   414 SLEGEPRKVVLHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELQRGDQILSVNGIDLRGASHEQAAAALKGAGQTVTIIAQYQPEDYARFEAKIHDLREQMMNHSM 524
               SCOP domains d2h  e2a_ A: automated matches                                                                                  SCOP domains
               CATH domains 2he  2A00 A:-1-517  [code=2.30.42.10, no name defined]                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--.eeeeee.......eeeee......eeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhh..ee-------ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:421-502 UniProt: 421-502                                              ---------------------- PROSITE
           Transcript 1 (1) 1.27----------------------------------------------------Exon 1.29a  PDB: A:470-504         -------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.28  PDB: A:419-469 UniProt: 417-469           ----------------------------------Exon 1.35a            Transcript 1 (2)
                 2he2 A  -1 SME--PRKVVLHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELQRGDQILSVNGIDLRGASHEQAAAALKGAGQTVTIIAQYQPEDYARFEAKIHET-------SV 517
                             ||  | 423       433       443       453       463       473       483       493       503       513 |     516 
                             0|  |                                                                                             515     516 
                            418  |                                                                                                         
                               419                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with DLG2_HUMAN | Q15700 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:108
                                   426       436       446       456       466       476       486       496       506       516        
           DLG2_HUMAN   417 GEPRKVVLHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELQRGDQILSVNGIDLRGASHEQAAAALKGAGQTVTIIAQYQPEDYARFEAKIHDLREQMMNHSM 524
               SCOP domains d2he2b_ B: automated matches                                                                                 SCOP domains
               CATH domains 2he2B00 B:0-517  [code=2.30.42.10, no name defined]                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.......eeeee......eeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeeehhhhhhhhhhh..ee-------ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:421-502 UniProt: 421-502                                              ---------------------- PROSITE
           Transcript 1 (1) 1----------------------------------------------------Exon 1.29a  PDB: B:470-504         -------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.28  PDB: B:0-469 UniProt: 417-469             ----------------------------------Exon 1.35a            Transcript 1 (2)
                 2he2 B   0 MEPRKVVLHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELQRGDQILSVNGIDLRGASHEQAAAALKGAGQTVTIIAQYQPEDYARFEAKIHET-------SV 517
                            ||     426       436       446       456       466       476       486       496       506        |-      | 
                            0|                                                                                              515     516 
                           418                                                                                                          

   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
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HE2)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DLG2_HUMAN | Q15700)
molecular function
    GO:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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).
biological process
    GO:0046710    GDP metabolic process    The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
    GO:0046037    GMP metabolic process    The chemical reactions and pathways involving GMP, guanosine monophosphate.
    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:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    GO:0097120    receptor localization to synapse    Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    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:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0044224    juxtaparanode region of axon    A region of an axon near a node of Ranvier that is between the paranode and internode regions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic 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:0008076    voltage-gated potassium channel complex    A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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 Related Entries

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

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        DLG2_HUMAN | Q157002byg

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