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(-) Description

Title :  A ROLE OF THE LOWE SYNDROME PROTEIN OCRL IN EARLY STEPS OF THE ENDOCYTIC PATHWAY
 
Authors :  Y. Mao, K. S. Erdman, H. J. Mccrea, P. De Camilli
Date :  07 Aug 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Endocytosis, Clathrin, Appl1, Phosphoinositide, Ash, Rhogap, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. S. Erdmann, Y. Mao, H. J. Mccrea, R. Zoncu, S. Lee, S. Paradise, J. Modregger, D. Biemesderfer, D. Toomre, P. De Camilli
A Role Of The Lowe Syndrome Protein Ocrl In Early Steps Of The Endocytic Pathway
Dev. Cell V. 13 377 2007
PubMed-ID: 17765681  |  Reference-DOI: 10.1016/J.DEVCEL.2007.08.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1
    ChainsA
    EC Number3.1.3.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX6P-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentASH-RHOGAP-LIKE TANDEM DOMAINS
    GeneOCRL, INPP5F, OCRL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOCRL;
LOWE OCULOCEREBRORENAL SYNDROME PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2QV2)

(-) Sites  (0, 0)

(no "Site" information available for 2QV2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QV2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844AN32K
2UniProtVAR_010188I768NOCRL_HUMANUnclassified (OCRL)  ---AI209N
3UniProtVAR_010189A797POCRL_HUMANUnclassified (OCRL)  ---AA238P
4UniProtVAR_064792P799LOCRL_HUMANDisease (DD2)  ---AP240L
5UniProtVAR_064793P801LOCRL_HUMANDisease (OCRL)  ---AP242L
6UniProtVAR_064794L891ROCRL_HUMANDisease (OCRL)137853845AL332R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844AN32K
2UniProtVAR_010188I768NOCRL_HUMANUnclassified (OCRL)  ---AI209N
3UniProtVAR_010189A797POCRL_HUMANUnclassified (OCRL)  ---AA238P
4UniProtVAR_064792P799LOCRL_HUMANDisease (DD2)  ---AP240L
5UniProtVAR_064793P801LOCRL_HUMANDisease (OCRL)  ---AP242L
6UniProtVAR_064794L891ROCRL_HUMANDisease (OCRL)137853845AL332R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.OCRL_HUMAN721-901  1A:170-339
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.OCRL_HUMAN721-901  2A:170-339

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003711132aENSE00001518494X:128674252-128674455204OCRL_HUMAN1-13130--
1.3aENST000003711133aENSE00001454376X:128674721-12867480080OCRL_HUMAN14-40270--
1.4ENST000003711134ENSE00001613852X:128678935-12867901480OCRL_HUMAN40-67280--
1.5aENST000003711135aENSE00001633886X:128682540-12868257839OCRL_HUMAN67-80140--
1.7ENST000003711137ENSE00000828196X:128691302-128691412111OCRL_HUMAN80-117380--
1.8ENST000003711138ENSE00000828195X:128691838-12869192790OCRL_HUMAN117-147310--
1.9ENST000003711139ENSE00000828194X:128692610-128692730121OCRL_HUMAN147-187410--
1.10bENST0000037111310bENSE00000828193X:128692817-128692978162OCRL_HUMAN187-241550--
1.11ENST0000037111311ENSE00000828192X:128694527-128694628102OCRL_HUMAN241-275350--
1.12ENST0000037111312ENSE00000828191X:128695156-128695270115OCRL_HUMAN275-313390--
1.13ENST0000037111313ENSE00000828190X:128696361-128696477117OCRL_HUMAN314-352390--
1.14ENST0000037111314ENSE00000828189X:128696576-128696763188OCRL_HUMAN353-415630--
1.15ENST0000037111315ENSE00000828188X:128699749-128699860112OCRL_HUMAN415-452380--
1.16aENST0000037111316aENSE00000828187X:128701231-128701340110OCRL_HUMAN453-489370--
1.17ENST0000037111317ENSE00001795169X:128703241-128703376136OCRL_HUMAN489-534460--
1.18ENST0000037111318ENSE00000828185X:128709117-128709227111OCRL_HUMAN535-571371A:9-124
1.19ENST0000037111319ENSE00000828184X:128709874-128710039166OCRL_HUMAN572-627561A:13-68 (gaps)56
1.20bENST0000037111320bENSE00000828183X:128710294-128710529236OCRL_HUMAN627-705791A:68-146 (gaps)79
1.21ENST0000037111321ENSE00001454375X:128718321-12871834424OCRL_HUMAN706-71381A:147-1548
1.23ENST0000037111323ENSE00000828182X:128720979-128721095117OCRL_HUMAN714-752391A:155-193 (gaps)39
1.24ENST0000037111324ENSE00000828181X:128722156-12872224085OCRL_HUMAN753-781291A:194-22229
1.25ENST0000037111325ENSE00000828180X:128722863-128722990128OCRL_HUMAN781-823431A:222-26443
1.26bENST0000037111326bENSE00000828179X:128723822-128723933112OCRL_HUMAN824-861381A:265-30238
1.27cENST0000037111327cENSE00001170507X:128724123-1287265382416OCRL_HUMAN861-901411A:302-33938

(-) 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:305
 aligned with OCRL_HUMAN | Q01968 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:331
                                   577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897 
           OCRL_HUMAN   568 SRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPSCFGTSLEALCRMKRPIREVPVTKLIDLEEDSFLEKEKSLLQMVPLDEGASERPLQVPKEIWLLVDHLFKYACHQEDLFQTPGMQEELQQIIDCLDTSIPETIPGSNHSVAEALLIFLEALPEPVICYELYQRCLDSAYDPRICRQVISQLPRCHRNVFRYLMAFLRELLKFSEYNSVNANMIATLFTSLLLRPPPNLMARQTPSDRQRAIQFLLGFLLGS 898
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------RhoGAP-2qv2A01 A:176-319                                                                                                                        -------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....ee.......----------.............eeee..............eeee.....hhhhhhhh.....eee..--------.eeeeeee.......hhhhhh..........hhhhh.................--------......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N----------------------------P-L-L-----------------------------------------------------------------------------------------R------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------RHOGAP  PDB: A:170-339 UniProt: 721-901                                                                                                                                            PROSITE
           Transcript 1 (1) 1.18Exon 1.19  PDB: A:13-68 (gaps) UniProt: 572-627         ------------------------------------------------------------------------------1.21    Exon 1.23  PDB: A:155-193 (gaps)       Exon 1.24  PDB: A:194-222    ------------------------------------------Exon 1.26b  PDB: A:265-302            ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.20b  PDB: A:68-146 (gaps) UniProt: 627-705                              ---------------------------------------------------------------------------Exon 1.25  PDB: A:222-264 UniProt: 781-823 -------------------------------------Exon 1.27c  PDB: A:302-339             Transcript 1 (2)
                 2qv2 A   9 SRREFVFENVKFRQLQKEKFQISN----------IPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVL--------FLTISGNYLPSCFGTSLEALCRMKRPIREVPVTKLIDLEEDSFLEKEKSLLQM--------ERPLQVPKEIWLLVDHLFKYACHQEDLFQTPGMQEELQQIIDCLDTSIPETIPGSNHSVAEALLIFLEALPEPVICYELYQRCLDSAYDPRICRQVISQLPRCHRNVFRYLMAFLRELLKFSEYNSVNANMIATLFTSLLLRPPPNLMARQTPSDRQRAIQFLLGFLLGS 339
                                    18        28   |     -    |   48        58        68        78        88        98 |       -|      118       128       138       148       158  |      - |     178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338 
                                                  32         43                                                      100      109                                                 161      170                                                                                                                                                                         

   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  (0, 0)

(no "SCOP Domain" information available for 2QV2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QV2)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GAP (15)

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)
Chain A   (OCRL_HUMAN | Q01968)
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:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    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:0052745    inositol phosphate phosphatase activity    Catalysis of the reaction: inositol phosphate(n) + H2O = inositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from an inositol phosphate.
    GO:0052659    inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0052658    inositol-1,4,5-trisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + H2O = 1D-myo-inositol 1,4-bisphosphate + phosphate.
    GO:0004439    phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
    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:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    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: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:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    GO:0005798    Golgi-associated vesicle    Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0001750    photoreceptor outer segment    The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
    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:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OCRL_HUMAN | Q019682kie 3qbt 3qis 4cmn

(-) Related Entries Specified in the PDB File

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