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(-) Description

Title :  COMPLEX OF THE 2ND AND 3RD LIM DOMAINS OF TES WITH THE EVH1 DOMAIN OF MENA AND THE N-TERMINAL DOMAIN OF ACTIN-LIKE PROTEIN ARP7A
 
Authors :  P. P. Knowles, D. C. Briggs, J. Murray-Rust, N. Q. Mcdonald
Date :  03 Sep 10  (Deposition) - 26 Jan 11  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,M,T
Keywords :  Metal-Binding Protein, Cytoskeleton, Focal Adhesion, Acrosome, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Boeda, P. P. Knowles, D. C. Briggs, J. Murray-Rust, E. Soriano, B. K. Garvalov, N. Q. Mcdonald, M. Way
Molecular Recognition Of The Tes Lim2-3 Domains By The Actin-Related Protein Arp7A.
J. Biol. Chem. V. 286 11543 2011
PubMed-ID: 21278383  |  Reference-DOI: 10.1074/JBC.M110.171264

(-) Compounds

Molecule 1 - ACTIN-LIKE PROTEIN 7A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMW172
    Expression System StrainFB810
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-65
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymARP7A, ACTIN-LIKE-7-ALPHA
 
Molecule 2 - ENABLED HOMOLOG
    ChainsM
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMW172
    Expression System StrainFB810
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEVH1 DOMAIN, RESIDUES 1-115
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMENA
 
Molecule 3 - TESTIN
    ChainsT
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMW172
    Expression System StrainFB810
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLIM DOMAINS 2 AND 3, RESIDUES 296-421
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTESS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AMT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1ZN5Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS T:301 , CYS T:304 , HIS T:322 , HIS T:325BINDING SITE FOR RESIDUE ZN T 1422
2AC2SOFTWARECYS T:328 , CYS T:331 , CYS T:349 , CYS T:352BINDING SITE FOR RESIDUE ZN T 1423
3AC3SOFTWARECYS T:361 , CYS T:364 , HIS T:383 , CYS T:388BINDING SITE FOR RESIDUE ZN T 1424
4AC4SOFTWARECYS T:391 , CYS T:394 , CYS T:412 , CYS T:416BINDING SITE FOR RESIDUE ZN T 1425
5AC5SOFTWAREHIS A:46 , CYS T:393 , CYS T:416 , HOH T:2027BINDING SITE FOR RESIDUE ZN T 1426

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031425R45CACL7A_HUMANPolymorphism368653764AR45C

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

(-) PROSITE Motifs  (3, 4)

Asymmetric/Biological Unit (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WH1PS50229 WH1 domain profile.ENAH_HUMAN1-111  1M:1-111
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.TES_HUMAN236-275
301-335
  1-
T:301-335
3LIM_DOMAIN_2PS50023 LIM domain profile.TES_HUMAN299-359
234-297
362-421
  2T:299-359
-
T:362-421

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003582041aENSE00001915255chr7:115850547-115850788242TES_HUMAN1-990--
1.3ENST000003582043ENSE00001748001chr7:115874588-11587467386TES_HUMAN10-38290--
1.4aENST000003582044aENSE00001801236chr7:115889074-115889326253TES_HUMAN38-122850--
1.5bENST000003582045bENSE00000919364chr7:115890215-115890550336TES_HUMAN123-2341120--
1.6cENST000003582046cENSE00000919366chr7:115891814-115892029216TES_HUMAN235-306721T:297-30610
1.7aENST000003582047aENSE00000919368chr7:115892372-115892530159TES_HUMAN307-359531T:307-35953
1.8dENST000003582048dENSE00001864576chr7:115897348-1158988371490TES_HUMAN360-421621T:360-42162

2.1aENST000003668441aENSE00001418664chr1:225840844-225840388457ENAH_HUMAN1-221M:1-22
2.3ENST000003668443ENSE00001674332chr1:225755116-225754951166ENAH_HUMAN2-57561M:2-5756
2.4ENST000003668444ENSE00001366252chr1:225742785-225742608178ENAH_HUMAN58-117601M:58-11356
2.6ENST000003668446ENSE00001236446chr1:225718340-22571825685ENAH_HUMAN117-145290--
2.7aENST000003668447aENSE00001848744chr1:225707267-225706900368ENAH_HUMAN145-2681240--
2.8bENST000003668448bENSE00001129404chr1:225705008-225704898111ENAH_HUMAN268-305380--
2.9bENST000003668449bENSE00001129400chr1:225702602-225702298305ENAH_HUMAN305-4061020--
2.10ENST0000036684410ENSE00001015553chr1:225700718-225700573146ENAH_HUMAN407-455490--
2.11aENST0000036684411aENSE00001015549chr1:225700416-22570035958ENAH_HUMAN455-474200--
2.12ENST0000036684412ENSE00001015556chr1:225699561-22569951349ENAH_HUMAN475-491170--
2.14ENST0000036684414ENSE00001015555chr1:225695719-22569565367ENAH_HUMAN491-513230--
2.15ENST0000036684415ENSE00001418158chr1:225692755-22569269363ENAH_HUMAN513-534220--
2.16bENST0000036684416bENSE00001015551chr1:225688772-22568869479ENAH_HUMAN534-560270--
2.17ENST0000036684417ENSE00001015550chr1:225686106-22568604958ENAH_HUMAN561-580200--
2.18fENST0000036684418fENSE00001442743chr1:225685514-2256805384977ENAH_HUMAN580-591120--

(-) 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 A from PDB  Type:PROTEIN  Length:22
 aligned with ACL7A_HUMAN | Q9Y615 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:22
                                    37        47  
          ACL7A_HUMAN    28 LQTASLRDGPAKRAVWVRHTSS  49
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .ee..ee....ee.eee..... Sec.struct. author
                 SAPs(SNPs) -----------------C---- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 2xqn A  28 LQTASLRDGPAKRAVWVRHTSS  49
                                    37        47  

Chain M from PDB  Type:PROTEIN  Length:116
 aligned with ENAH_HUMAN | Q8N8S7 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:116
                               1                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107      
           ENAH_HUMAN     - ---MSEQSICQARAAVMVYDDANKKWVPAGGSTGFSRVHIYHHTGNNTFRVVGRKIQDHQVVINCAIPKGLKYNQATQTFHQWRDARQVYGLNFGSKEDANVFASAMMHALEVLNS 113
               SCOP domains d2xqnm_ M: Enabled                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---WH1-2xqnM01 M:1-108                                                                                         ----- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeeee....eeee.hhh...eeeeeeee....eeeeeeee.....eeeeee.............eeeee....eeeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---WH1  PDB: M:1-111 UniProt: 1-111                                                                               -- PROSITE
           Transcript 2 (1) ---2.-------------------------------------------------------Exon 2.4  PDB: M:58-113 UniProt: 58-117 [INCOMPLETE]     Transcript 2 (1)
           Transcript 2 (2) ----Exon 2.3  PDB: M:2-57 UniProt: 2-57                     -------------------------------------------------------- Transcript 2 (2)
                 2xqn M  -2 AARMSEQSICQARAAVMVYDDANKKWVPAGGSTGFSRVHIYHHTGNNTFRVVGRKIQDHQVVINCAIPKGLKYNQATQTFHQWRDARQVYGLNFGSKEDANVFASAMMHALEVLNS 113
                                     7        17        27        37        47        57        67        77        87        97       107      

Chain T from PDB  Type:PROTEIN  Length:125
 aligned with TES_HUMAN | Q9UGI8 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:125
                                   306       316       326       336       346       356       366       376       386       396       406       416     
            TES_HUMAN   297 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRMS 421
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------LIM-2xqnT01 T:361-420                                       - Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------LIM-2xqnT02 T:361-420                                       - Pfam domains (2)
         Sec.struct. author ................eeee..eeehhhhh............eeeee..eeeehhhhhhhh................eeee..eeee..................eeeee..eee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----LIM_DOMAIN_1  PDB: T:301-335       --------------------------LIM_DOMAIN_2  PDB: T:362-421 UniProt: 362-421                PROSITE (1)
                PROSITE (2) L-LIM_DOMAIN_2  PDB: T:299-359 UniProt: 299-359                -------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.6c Exon 1.7a  PDB: T:307-359 UniProt: 307-359           Exon 1.8d  PDB: T:360-421 UniProt: 360-421                     Transcript 1
                 2xqn T 297 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRMS 421
                                   306       316       326       336       346       356       366       376       386       396       406       416     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: PH (111)
(-)
Family: LIM (23)
2aLIM-2xqnT01T:361-420
2bLIM-2xqnT02T:361-420

(-) Gene Ontology  (25, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACL7A_HUMAN | Q9Y615)
molecular function
    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:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0001673    male germ cell nucleus    The nucleus of a male germ cell, a reproductive cell in males.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Chain M   (ENAH_HUMAN | Q8N8S7)
molecular function
    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:0050699    WW domain binding    Interacting selectively and non-covalently with a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    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: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.

Chain T   (TES_HUMAN | Q9UGI8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENAH_HUMAN | Q8N8S72ho2 2iyb 4my6 5n91 5n9c 5n9p 5naj 5nbf 5ncf
        TES_HUMAN | Q9UGI82iyb

(-) Related Entries Specified in the PDB File

2iyb STRUCTURE OF COMPLEX BETWEEN THE 3RD LIM DOMAIN OF TES AND THE EVH1 DOMAIN OF MENA