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(-) Description

Title :  STRUCTURAL FLEXIBILITY OF SHANK PDZ DOMAIN IS IMPORTANT FOR ITS BINDING TO DIFFERENT LIGANDS
 
Authors :  J. H. Lee, H. Park, S. J. Park, H. J. Kim, S. H. Eom
Date :  30 Jan 11  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Pdz Domain, Protein-Protein Interaction, Beta-Pix, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Lee, H. Park, S. J. Park, H. J. Kim, S. H. Eom
The Structural Flexibility Of The Shank1 Pdz Domain Is Important For Its Binding To Different Ligands
Biochem. Biophys. Res. Commun. V. 407 207 2011
PubMed-ID: 21376703  |  Reference-DOI: 10.1016/J.BBRC.2011.02.141

(-) Compounds

Molecule 1 - SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPDZ DOMAIN
    GeneSHANK1
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymSHANK1, GKAP/SAPAP-INTERACTING PROTEIN, SPANK-1, SOMATOSTATIN RECEPTOR-INTERACTING PROTEIN, SSTR-INTERACTING PROTEIN, SSTRIP, SYNAMON
 
Molecule 2 - BETA-PIX
    ChainsC, D
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3QJM)

(-) Sites  (0, 0)

(no "Site" information available for 3QJM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QJM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QJM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QJM)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SHAN1_RAT663-757
 
  2A:663-757
B:663-757
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SHAN1_RAT663-757
 
  1A:663-757
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SHAN1_RAT663-757
 
  1-
B:663-757

(-) Exons   (4, 7)

Asymmetric Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000261001ENSRNOE00000272017chr1:94791887-9479192034SHAN1_RAT-00--
1.2ENSRNOT000000261002ENSRNOE00000272009chr1:94794319-94794616298SHAN1_RAT1-85850--
1.3ENSRNOT000000261003ENSRNOE00000186599chr1:94794778-94794981204SHAN1_RAT86-153680--
1.4ENSRNOT000000261004ENSRNOE00000300486chr1:94795393-9479546472SHAN1_RAT154-177240--
1.5ENSRNOT000000261005ENSRNOE00000272001chr1:94797836-94797944109SHAN1_RAT178-214370--
1.6ENSRNOT000000261006ENSRNOE00000271993chr1:94798161-94798312152SHAN1_RAT214-264510--
1.7ENSRNOT000000261007ENSRNOE00000186706chr1:94800979-94801146168SHAN1_RAT265-320560--
1.8ENSRNOT000000261008ENSRNOE00000313183chr1:94801526-94801642117SHAN1_RAT321-359390--
1.9ENSRNOT000000261009ENSRNOE00000186782chr1:94807204-9480728178SHAN1_RAT360-385260--
1.10ENSRNOT0000002610010ENSRNOE00000271239chr1:94807523-9480758967SHAN1_RAT386-408230--
1.11ENSRNOT0000002610011ENSRNOE00000271234chr1:94807849-94808179331SHAN1_RAT408-5181110--
1.12ENSRNOT0000002610012ENSRNOE00000271228chr1:94808929-94809122194SHAN1_RAT518-583660--
1.13ENSRNOT0000002610013ENSRNOE00000271223chr1:94814184-94814297114SHAN1_RAT583-621390--
1.14ENSRNOT0000002610014ENSRNOE00000271216chr1:94814441-9481451676SHAN1_RAT621-646260--
1.15ENSRNOT0000002610015ENSRNOE00000271210chr1:94814931-9481495727SHAN1_RAT646-655101-
B:654-655
-
2
1.17ENSRNOT0000002610017ENSRNOE00000271202chr1:94823419-9482350183SHAN1_RAT655-683292A:656-681
B:655-681
26
27
1.18ENSRNOT0000002610018ENSRNOE00000271197chr1:94823745-94823869125SHAN1_RAT683-724422A:687-724
B:689-724
38
36
1.19ENSRNOT0000002610019ENSRNOE00000271186chr1:94824379-94824514136SHAN1_RAT725-770462A:725-758
B:725-758
34
34
1.20ENSRNOT0000002610020ENSRNOE00000271179chr1:94825010-9482509081SHAN1_RAT770-797280--
1.21ENSRNOT0000002610021ENSRNOE00000271147chr1:94825645-9482566824SHAN1_RAT797-80590--
1.22ENSRNOT0000002610022ENSRNOE00000271174chr1:94825852-9482592069SHAN1_RAT805-828240--
1.23ENSRNOT0000002610023ENSRNOE00000271166chr1:94826271-94826389119SHAN1_RAT828-867400--
1.24ENSRNOT0000002610024ENSRNOE00000271162chr1:94832245-9483234197SHAN1_RAT868-900330--
1.25ENSRNOT0000002610025ENSRNOE00000271157chr1:94832865-948359523088SHAN1_RAT900-192910300--
1.27ENSRNOT0000002610027ENSRNOE00000187264chr1:94838875-948405841710SHAN1_RAT1929-21672390--

(-) 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:98
 aligned with SHAN1_RAT | Q9WV48 from UniProtKB/Swiss-Prot  Length:2167

    Alignment length:103
                                   665       675       685       695       705       715       725       735       745       755   
            SHAN1_RAT   656 DYIIKEKTVLLQKKDSEGFGFVLRGAKAQTPIEEFTPTPAFPALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR 758
               SCOP domains d3qjma_ A: Shank1, PDZ dom     ain                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee........eeeee.-----.............eeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:663-757 UniProt: 663-757                                                           - PROSITE
           Transcript 1 (1) ---------------------------Exon 1.18  PDB: A:687-724 UniProt: 683-724Exon 1.19  PDB: A:725-758          Transcript 1 (1)
           Transcript 1 (2) Exon 1.17  PDB: A:656-681   --------------------------------------------------------------------------- Transcript 1 (2)
                 3qjm A 656 DYIIKEKTVLLQKKDSEGFGFVLRGA-----IEEFTPTPAFPALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR 758
                                   665       675     |   - |     695       705       715       725       735       745       755   
                                                   681   687                                                                       

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with SHAN1_RAT | Q9WV48 from UniProtKB/Swiss-Prot  Length:2167

    Alignment length:105
                                   663       673       683       693       703       713       723       733       743       753     
            SHAN1_RAT   654 GSDYIIKEKTVLLQKKDSEGFGFVLRGAKAQTPIEEFTPTPAFPALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR 758
               SCOP domains d3qjmb_ B: Shank1, PDZ domai       n                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------PDZ-3qjmB01 B:663-7       54                                                                ---- Pfam domains (1)
           Pfam domains (2) ---------PDZ-3qjmB02 B:663-7       54                                                                ---- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee........eeeee.-------...........eeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDZ  PDB: B:663-757 UniProt: 663-757                                                           - PROSITE
           Transcript 1 (1) 1.---------------------------Exon 1.18  PDB: B:689-724 UniProt: 683-724Exon 1.19  PDB: B:725-758          Transcript 1 (1)
           Transcript 1 (2) -Exon 1.17  PDB: B:655-681    --------------------------------------------------------------------------- Transcript 1 (2)
                 3qjm B 654 GSDYIIKEKTVLLQKKDSEGFGFVLRGA-------EFTPTPAFPALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR 758
                                   663       673       | -     | 693       703       713       723       733       743       753     
                                                     681     689                                                                     

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .eee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3qjm C 642 DETNL 646

Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .eee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3qjm D 642 DETNL 646

   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  (0, 0)

(no "CATH Domain" information available for 3QJM)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-3qjmB01B:663-754
1bPDZ-3qjmB02B:663-754

(-) Gene Ontology  (46, 46)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SHAN1_RAT | Q9WV48)
molecular function
    GO:0030160    GKAP/Homer scaffold activity    Functions as a physical support bridging the N-methyl-D-aspartate receptor-PSD-95-GKAP complex and the mGluR-Homer complex, which are involved in receptor signaling in synapses.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0071532    ankyrin repeat binding    Interacting selectively and non-covalently with an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0031877    somatostatin receptor binding    Interacting selectively and non-covalently with a somatostatin receptor.
biological process
    GO:0030534    adult behavior    Behavior in a fully developed and mature organism.
    GO:0008306    associative learning    Learning by associating a stimulus (the cause) with a particular outcome (the effect).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007016    cytoskeletal anchoring at plasma membrane    A cytoskeleton organization process that directly or indirectly links cytoskeletal filaments to the plasma membrane.
    GO:0060997    dendritic spine morphogenesis    The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0050894    determination of affect    Any process in which an emotional response is associated with a particular sensory stimulation.
    GO:0046959    habituation    A decrease in a behavioral response to a repeated stimulus. This is exemplified by the failure of a person to show a startle response to a loud noise that has been repeatedly presented.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0032232    negative regulation of actin filament bundle assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles.
    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:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0042048    olfactory behavior    The behavior of an organism in response to an odor.
    GO:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0035418    protein localization to synapse    Any process in which a protein 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:2000311    regulation of AMPA receptor activity    Any process that modulates the frequency, rate or extent of AMPA selective glutamate receptor activity.
    GO:0060013    righting reflex    A reflex process in which an animal immediately tries to turn over after being placed in a supine position.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    GO:0060074    synapse maturation    The process that organizes a synapse so that it attains its fully functional state. Synaptic maturation plays a critical role in the establishment of effective synaptic connections in early development.
    GO:0071625    vocalization behavior    The behavior in which an organism produces sounds by a mechanism involving its respiratory system.
cellular component
    GO:0017146    NMDA selective glutamate receptor complex    An 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. NMDA receptors are composed of assemblies of NR1 subunits (Figure 3) and NR2 subunits, which can be one of four separate gene products (NR2A-D). Expression of both subunits are required to form functional channels. The glutamate binding domain is formed at the junction of NR1 and NR2 subunits. NMDA receptors are permeable to calcium ions as well as being permeable to other ions. Thus NMDA receptor activation leads to a calcium influx into the post-synaptic cells, a signal thought to be crucial for the induction of NMDA-receptor dependent LTP and LTD.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SHAN1_RAT | Q9WV481q3o 1q3p 3l4f 3qjn

(-) Related Entries Specified in the PDB File

3qjn