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(-) Description

Title :  STRUCTURE OF OSH4P/KES1P IN COMPLEX WITH PHOSPHATIDYLINOSITOL 4-PHOSPHATE
 
Authors :  V. Delfosse, M. De Saint-Jean, D. Douguet, B. Antonny, G. Drin, W. Bour
Date :  04 Jul 11  (Deposition) - 23 Nov 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipid Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. De Saint-Jean, V. Delfosse, D. Douguet, G. Chicanne, B. Payrastre W. Bourguet, B. Antonny, G. Drin
Osh4P Exchanges Sterols For Phosphatidylinositol 4-Phosphat Between Lipid Bilayers.
J. Cell Biol. V. 195 965 2011
PubMed-ID: 22162133  |  Reference-DOI: 10.1083/JCB.201104062

(-) Compounds

Molecule 1 - PROTEIN KES1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T-3
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneKES1, LPI3C, OSH4, P2614, YPL145C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymOXYSTEROL-BINDING PROTEIN HOMOLOG 4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1T7M2Ligand/Ion(2R)-1-(HEPTADECANOYLOXY)-3-{[(R)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPAN-2-YL (5Z,8Z,11Z,14Z)-ICOSA-5,8,11,14-TETRAENOATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1T7M1Ligand/Ion(2R)-1-(HEPTADECANOYLOXY)-3-{[(R)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPAN-2-YL (5Z,8Z,11Z,14Z)-ICOSA-5,8,11,14-TETRAENOATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1T7M1Ligand/Ion(2R)-1-(HEPTADECANOYLOXY)-3-{[(R)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPAN-2-YL (5Z,8Z,11Z,14Z)-ICOSA-5,8,11,14-TETRAENOATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:24 , SER A:25 , SER A:26 , LEU A:27 , SER A:28 , ALA A:29 , GLN A:96 , GLU A:107 , LYS A:109 , ASN A:112 , HIS A:143 , HIS A:144 , ALA A:169 , LYS A:336 , GLU A:340 , ARG A:344 , HOH A:475 , HOH A:595 , HOH A:614BINDING SITE FOR RESIDUE T7M A 435
2AC2SOFTWARELEU B:24 , SER B:25 , SER B:26 , LEU B:27 , SER B:28 , ALA B:29 , ASN B:112 , HIS B:143 , HIS B:144 , LYS B:336 , ARG B:344 , HOH B:461BINDING SITE FOR RESIDUE T7M B 435

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:144 -Pro A:145
2His B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OSBPPS01013 Oxysterol-binding protein family signature.KES1_YEAST139-149
 
  2A:139-149
B:139-149
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OSBPPS01013 Oxysterol-binding protein family signature.KES1_YEAST139-149
 
  1A:139-149
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OSBPPS01013 Oxysterol-binding protein family signature.KES1_YEAST139-149
 
  1-
B:139-149

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL145C1YPL145C.1XVI:279698-2783941305KES1_YEAST1-4344342A:13-434 (gaps)
B:20-433 (gaps)
422
414

(-) 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:398
 aligned with KES1_YEAST | P35844 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:422
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432  
           KES1_YEAST    13 FLKSIASFNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYKEHCLIDPEVESPELARMLAVTKWFISTLKSQYCSRNESLGSEKKPLNPFLGELFVGKWENKEHPEFGETVLLSEQVSHHPPVTAFSIFNDKNKVKLQGYNQIKASFTKSLMLTVKQFGHTMLDIKDESYLVTPPPLHIEGILVASPFVELEGKSYIQSSTGLLCVIEFSGRGYFSGKKNSFKARIYKDSKDSKDKEKALYTISGQWSGSSKIIKANKKEESRLFYDAARIPAEHLNVKPLEEQHPLESRKAWYDVAGAIKLGDFNLIAKTKTELEETQRELRKEEEAKGISWQRRWFKDFDYSVTPEEGALVPEKDDTFLKLASALNLSTKNAPSGTLVGDKEDRKEDLSSIHWRFQRELWDEEKEIVL 434
               SCOP domains d3spwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhh..hhh.eeeee.hhhhhhhh.hhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh-------...eee......eeeeee..........eeeeeeeee....eeeeeeee....eeeeeeeeeeee.----..eeeeeeeeeeee..eeeee....ee.---------.ee..eeeeee....eeeeeee..----....eeeeeee...hhhhhhhhh.eeeeee...eeeeee..hhhhheeeee............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.........ee....hhhhhhhhhhh........................eeeeehhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------OSBP       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:13-434 (gaps) UniProt: 1-434 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 3spw A  13 FLKSIASFNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYKEHCLIDPEVESPELARMLAVTKWFISTLKSQYC-------SEKKPLNPFLGELFVGKWENKEHPEFGETVLLSEQVSHHPPVTAFSIFNDKNKVKLQGYNQIKASF----MLTVKQFGHTMLDIKDESYLVTPPPLHI---------VELEGKSYIQSSTGLLCVIEFSGR----GKKNSFKARIYKDSKDSKDKEKALYTISGQWSGSSKIIKANKKEESRLFYDAARIPAEHLNVKPLEEQHPLESRKAWYDVAGAIKLGDFNLIAKTKTELEETQRELRKEEEAKGISWQRRWFKDFDYSVTPEEGALVPEKDDTFLKLASALNLSTKNAPSGTLVGDKEDRKEDLSSIHWRFQRELWDEEKEIVL 434
                                    22        32        42        52        62        72        82        92     |   -   |   112       122       132       142       152       162        |-   |   182       192       202|        -|      222       232   |   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432  
                                                                                                                98     106                                                              171  176                        203       213                    236  241                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with KES1_YEAST | P35844 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:414
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
           KES1_YEAST    20 FNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYKEHCLIDPEVESPELARMLAVTKWFISTLKSQYCSRNESLGSEKKPLNPFLGELFVGKWENKEHPEFGETVLLSEQVSHHPPVTAFSIFNDKNKVKLQGYNQIKASFTKSLMLTVKQFGHTMLDIKDESYLVTPPPLHIEGILVASPFVELEGKSYIQSSTGLLCVIEFSGRGYFSGKKNSFKARIYKDSKDSKDKEKALYTISGQWSGSSKIIKANKKEESRLFYDAARIPAEHLNVKPLEEQHPLESRKAWYDVAGAIKLGDFNLIAKTKTELEETQRELRKEEEAKGISWQRRWFKDFDYSVTPEEGALVPEKDDTFLKLASALNLSTKNAPSGTLVGDKEDRKEDLSSIHWRFQRELWDEEKEIV 433
               SCOP domains d3spwb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh..hhh.eeeee.hhhhhhhh.hhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh--------..eee......eeeeee..........eeeeeeeee....eeeeeeee....eeeeeeeeeeee-----..eeeeeeeeeeee..eeeeee...eee.------..eee..eeeeee....eeeeeee..-----...eeeeeee.hhhhh.hhhhh.eeeeee...eeeeee......eeeeee............hhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee...............hhhhhhhhhhh.............hhhhhh.....eeeeehhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------OSBP       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:20-433 (gaps) UniProt: 1-434 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 3spw B  20 FNGDLSSLSAPPFILSPISLTEFSQYWAEHPELFLEPSFINDDNYKEHCLIDPEVESPELARMLAVTKWFISTLKSQYC--------EKKPLNPFLGELFVGKWENKEHPEFGETVLLSEQVSHHPPVTAFSIFNDKNKVKLQGYNQIKAS-----MLTVKQFGHTMLDIKDESYLVTPPPLHIE------PFVELEGKSYIQSSTGLLCVIEFSGR-----KKNSFKARIYKDSKDSKDKEKALYTISGQWSGSSKIIKANKKEESRLFYDAARIPAEHLNVKPLEEQHPLESRKAWYDVAGAIKLGDFNLIAKTKTELEETQRELRKEEEAKGISWQRRWFKDFDYSVTPEEGALVPEKDDTFLKLASALNLSTKNAPSGTLVGDKEDRKEDLSSIHWRFQRELWDEEKEIV 433
                                    29        39        49        59        69        79        89        |-       109       119       129       139       149       159       169|     |179       189       199    |    - |     219       229      |  -  |    249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
                                                                                                         98      107                                                            170   176                         204    211                      236   242                                                                                                                                                                                               

   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 3SPW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SPW)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KES1_YEAST | P35844)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0008142    oxysterol binding    Interacting selectively and non-covalently with oxysterol, an oxidized form of cholesterol.
    GO:0070300    phosphatidic acid binding    Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0015248    sterol transporter activity    Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
biological process
    GO:0035621    ER to Golgi ceramide transport    The directed movement of a ceramide from the endoplasmic reticulum (ER) to the Golgi. Ceramides are a class of lipid composed of sphingosine linked to a fatty acid.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    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:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0030011    maintenance of cell polarity    The maintenance of established anisotropic intracellular organization or cell growth patterns.
    GO:0034727    piecemeal microautophagy of nucleus    Degradation of a cell nucleus by lysosomal microautophagy.
    GO:0010922    positive regulation of phosphatase activity    Any process that increases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0006892    post-Golgi vesicle-mediated transport    The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.
    GO:0006665    sphingolipid metabolic process    The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    GO:0015918    sterol transport    The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KES1_YEAST | P358441zht 1zhw 1zhx 1zhy 1zhz 1zi7 4f4b 4fes 4jch

(-) Related Entries Specified in the PDB File

1zhz STRUCTURE OF YEAST OXYSTEROL BINDING PROTEIN OSH4 IN COMPLEX WITH ERGOSTEROL