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(-) Description

Title :  THE NOVEL BINDING MODE OF DLC1 AND TENSIN2 PTB DOMAIN
 
Authors :  C. Liu, L. Chen, G. Zhu
Date :  29 Jan 12  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Ptb, Dlc1, Hydrolase-Hydrolase Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Chen, C. Liu, F. C. F. Ko, N. Xu, I. O. -L. Ng, J. W. P. Yam, G. Zhu
Solution Structure Of The Ptb Domain Of Human Tensin2 In Complex With Deleted In Liver Cancer 1 (Dlc1) Peptide Reveals A Novel Peptide Binding Mode
J. Biol. Chem. 2012
PubMed: search  |  Reference-DOI: 10.1074/JBC.M112.360206

(-) Compounds

Molecule 1 - TENSIN-LIKE C1 DOMAIN-CONTAINING PHOSPHATASE
    ChainsA
    EC Number3.1.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET
    FragmentPTB DOMAIN, UNP RESIDUES 1263-1409
    GeneTENC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN HOMOLOG, C1-TEN, TENSIN-2
 
Molecule 2 - RHO GTPASE-ACTIVATING PROTEIN 7
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET
    FragmentUNP RESIDUES 811-824
    GeneDLC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDELETED IN LIVER CANCER 1 PROTEIN, DLC-1, HP PROTEIN, RHO- TYPE GTPASE-ACTIVATING PROTEIN 7, START DOMAIN-CONTAINING PROTEIN 12, STARD12, STAR-RELATED LIPID TRANSFER PROTEIN 12

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LOZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2LOZ)

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002762972bENSE00001189213chr8:13372395-13372111285RHG07_HUMAN-00--
1.3bENST000002762973bENSE00001388926chr8:13357705-133565581148RHG07_HUMAN1-3413410--
1.4ENST000002762974ENSE00000979612chr8:13259128-13258979150RHG07_HUMAN342-391500--
1.5bENST000002762975bENSE00001015479chr8:13251202-13251062141RHG07_HUMAN392-438470--
1.6aENST000002762976aENSE00001087081chr8:13162811-1316277834RHG07_HUMAN439-450120--
1.12ENST0000027629712ENSE00001189219chr8:12973166-1297309572RHG07_HUMAN450-474250--
1.13ENST0000027629713ENSE00001087061chr8:12968332-1296825182RHG07_HUMAN474-501280--
1.14ENST0000027629714ENSE00001087065chr8:12960362-1296029964RHG07_HUMAN501-522220--
1.15eENST0000027629715eENSE00001087057chr8:12958279-129568561424RHG07_HUMAN523-9974751B:367-38014
1.16ENST0000027629716ENSE00001087059chr8:12956084-12955908177RHG07_HUMAN997-1056600--
1.18ENST0000027629718ENSE00001087055chr8:12952754-12952595160RHG07_HUMAN1056-1109540--
1.19cENST0000027629719cENSE00001087071chr8:12952466-12952268199RHG07_HUMAN1110-1176670--
1.20ENST0000027629720ENSE00001087051chr8:12950334-12950121214RHG07_HUMAN1176-1247720--
1.21ENST0000027629721ENSE00001087050chr8:12948941-12948827115RHG07_HUMAN1247-1285390--
1.22ENST0000027629722ENSE00001087069chr8:12947979-12947761219RHG07_HUMAN1286-1358730--
1.23bENST0000027629723bENSE00001087054chr8:12946213-12945996218RHG07_HUMAN1359-1431730--
1.24aENST0000027629724aENSE00001087052chr8:12943972-12943799174RHG07_HUMAN1431-1489590--
1.25eENST0000027629725eENSE00001216909chr8:12943440-129408702571RHG07_HUMAN1489-1528400--

2.3ENST000003142503ENSE00002176967chr12:53443680-53444044365TNS2_HUMAN1-25250--
2.4ENST000003142504ENSE00001702661chr12:53445639-53445747109TNS2_HUMAN26-62370--
2.5ENST000003142505ENSE00001602732chr12:53446239-5344627638TNS2_HUMAN62-74130--
2.6ENST000003142506ENSE00001706663chr12:53447195-5344723339TNS2_HUMAN75-87130--
2.7ENST000003142507ENSE00001646683chr12:53447558-5344759639TNS2_HUMAN88-100130--
2.8ENST000003142508ENSE00001602842chr12:53447749-5344779850TNS2_HUMAN101-117170--
2.9ENST000003142509ENSE00001622467chr12:53448054-53448225172TNS2_HUMAN117-174580--
2.10ENST0000031425010ENSE00000838131chr12:53448970-5344902051TNS2_HUMAN175-191170--
2.11aENST0000031425011aENSE00000938905chr12:53449352-53449474123TNS2_HUMAN192-232410--
2.11cENST0000031425011cENSE00000838133chr12:53449565-5344962965TNS2_HUMAN233-254220--
2.12ENST0000031425012ENSE00000838134chr12:53450797-5345088084TNS2_HUMAN254-282290--
2.13ENST0000031425013ENSE00000746463chr12:53451351-53451463113TNS2_HUMAN282-320390--
2.14ENST0000031425014ENSE00000746465chr12:53451557-5345161761TNS2_HUMAN320-340210--
2.15ENST0000031425015ENSE00000746467chr12:53451811-5345188676TNS2_HUMAN340-365260--
2.16ENST0000031425016ENSE00000746468chr12:53452100-53452229130TNS2_HUMAN366-409440--
2.17ENST0000031425017ENSE00000746469chr12:53452356-5345242166TNS2_HUMAN409-431230--
2.18ENST0000031425018ENSE00000746470chr12:53452498-53452611114TNS2_HUMAN431-469390--
2.19cENST0000031425019cENSE00000746471chr12:53452831-534540421212TNS2_HUMAN469-8734050--
2.20ENST0000031425020ENSE00000746472chr12:53454189-53454339151TNS2_HUMAN873-923510--
2.21ENST0000031425021ENSE00000746473chr12:53454459-53455048590TNS2_HUMAN923-11201980--
2.22ENST0000031425022ENSE00000491479chr12:53455164-5345525390TNS2_HUMAN1120-1150310--
2.23ENST0000031425023ENSE00000746475chr12:53455599-53455724126TNS2_HUMAN1150-1192430--
2.24ENST0000031425024ENSE00000746476chr12:53455937-5345602993TNS2_HUMAN1192-1223320--
2.25ENST0000031425025ENSE00000746477chr12:53456160-5345623778TNS2_HUMAN1223-1249270--
2.26bENST0000031425026bENSE00000838135chr12:53456404-5345648178TNS2_HUMAN1249-1275271A:1263-127513
2.27aENST0000031425027aENSE00000838136chr12:53456873-53457041169TNS2_HUMAN1275-1331571A:1275-133157
2.28ENST0000031425028ENSE00000746494chr12:53457133-5345720169TNS2_HUMAN1331-1354241A:1331-135424
2.29ENST0000031425029ENSE00000746496chr12:53457347-5345737630TNS2_HUMAN1354-1364111A:1354-136411
2.30aENST0000031425030aENSE00001411522chr12:53457528-53458155628TNS2_HUMAN1364-1409461A:1364-140946

(-) Sequences/Alignments

NMR Structure
   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:147
 aligned with TNS2_HUMAN | Q63HR2 from UniProtKB/Swiss-Prot  Length:1409

    Alignment length:147
                                  1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402       
          TNS2_HUMAN   1263 MSTAADLLRQGAACSVLYLTSVETESLTGPQAVARASSAALSCSPRPTPAVVHFKVSAQGITLTDNQRKLFFRRHYPVNSITFSSTDPQDRRWTNPDGTTSKIFGFVAKKPGSPWENVCHLFAELDPDQPAGAIVTFITKVLLGQRK 1409
               SCOP domains d2loza_ A: Tensin                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeeeeeeeee....hhhhhhhhhhhhhhhh......eeeeeeee..eeeee...........ee...eeeee......eee.....eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.26b   -------------------------------------------------------Exon 2.28               ---------Exon 2.30a  PDB: A:1364-1409                   Transcript 2 (1)
           Transcript 2 (2) ------------Exon 2.27a  PDB: A:1275-1331 UniProt: 1275-1331          ----------------------Exon 2.29  --------------------------------------------- Transcript 2 (2)
                2loz A 1263 MSTAADLLRQGAACSVLYLTSVETESLTGPQAVARASSAALSCSPRPTPAVVHFKVSAQGITLTDNQRKLFFRRHYPVNSITFSSTDPQDRRWTNPDGTTSKIFGFVAKKPGSPWENVCHLFAELDPDQPAGAIVTFITKVLLGQRK 1409
                                  1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402       

Chain B from PDB  Type:PROTEIN  Length:14
 aligned with RHG07_HUMAN | Q96QB1 from UniProtKB/Swiss-Prot  Length:1528

    Alignment length:14
                                   820    
         RHG07_HUMAN    811 EDHKPGTFPKALTN  824
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
               Transcript 1 Exon 1.15e     Transcript 1
                2loz B  367 EDHKPGTFPKALTN  380
                                   376    

   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)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 53)

NMR Structure(hide GO term definitions)
Chain A   (TNS2_HUMAN | Q63HR2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0019725    cellular homeostasis    Any process involved in the maintenance of an internal steady state at the level of the cell.
    GO:0032963    collagen metabolic process    The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0048871    multicellular organismal homeostasis    Any process involved in the maintenance of an internal steady state at the level of the multicellular organism.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0014850    response to muscle activity    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 muscle activity stimulus.
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: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: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: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.

Chain B   (RHG07_HUMAN | Q96QB1)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0021575    hindbrain morphogenesis    The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
    GO:0035024    negative regulation of Rho protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0051895    negative regulation of focal adhesion assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0051497    negative regulation of stress fiber assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1900119    positive regulation of execution phase of apoptosis    Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
    GO:0035307    positive regulation of protein dephosphorylation    Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    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:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TNS2_HUMAN | Q63HR2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RHG07_HUMAN | Q96QB12dky 2gyt 2kap 3kuq 5fzt
        TNS2_HUMAN | Q63HR22dkq 2kno 2l6k 3hqc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2LOZ)