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(-) Description

Title :  KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 8 (EPHA8)
 
Authors :  J. R. Walker, L. Yermekbayeva, J. Kania, C. Bountra, J. Weigelt, C. H. Ar A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics C (Sgc)
Date :  27 Nov 09  (Deposition) - 15 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Atp-Binding, Kinase, Nucleotide-Binding, Receptor, Transferase, Phosphorylation, Transmembrane, Tyrosine-Protein Kinase, Structural Genomics Consortium, Sgc, Glycoprotein, Membrane, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, L. Yermekbayeva, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Kinase Domain Of Human Ephrin Type-A Receptor 8 (Epha8)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 8
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN (UNP RESIDUES 602-909)
    GeneEEK, EPHA8, HEK3, KIAA1459
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTYR AT POSITION 793
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR EEK, EPH- AND ELK-RELATED KINASE, HEK3
 
Molecule 2 - EPHRIN TYPE-A RECEPTOR 8
    ChainsB
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN (UNP RESIDUES 602-909)
    GeneEEK, EPHA8, HEK3, KIAA1459
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPTR AT POSITION 793
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR EEK, EPH- AND ELK-RELATED KINASE, HEK3

 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  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2GOL1Ligand/IonGLYCEROL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2GOL1Ligand/IonGLYCEROL
3PTR-1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2GOL-1Ligand/IonGLYCEROL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:11 , HOH A:104 , HOH A:298 , HIS A:693 , ARG A:742 , ARG A:749BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREGLU A:648 , CYS A:650 , ILE A:666 , ALA A:668 , MET A:710BINDING SITE FOR RESIDUE BME A 401
3AC3SOFTWAREHOH A:58 , TYR A:651 , TYR A:715 , MET A:716 , GLU A:717 , GLY A:719BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREHOH A:215 , ARG A:884 , SER A:886 , ARG B:884BINDING SITE FOR RESIDUE SO4 A 910
5AC5SOFTWAREGLU B:648 , CYS B:650BINDING SITE FOR RESIDUE BME B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042158P860LEPHA8_HUMANUnclassified  ---A/BP860L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042158P860LEPHA8_HUMANUnclassified  ---AP860L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042158P860LEPHA8_HUMANUnclassified  ---BP860L

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHA8_HUMAN641-667
 
  2A:641-667
B:641-667
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA8_HUMAN756-768
 
  2A:756-768
B:756-768
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHA8_HUMAN641-667
 
  1A:641-667
-
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA8_HUMAN756-768
 
  1A:756-768
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHA8_HUMAN641-667
 
  1-
B:641-667
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA8_HUMAN756-768
 
  1-
B:756-768

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000001662441ENSE00001156951chr1:22890057-22890222166EPHA8_HUMAN1-32320--
1.2ENST000001662442ENSE00000388454chr1:22895782-2289584665EPHA8_HUMAN32-53220--
1.3ENST000001662443ENSE00001131811chr1:22902710-22903373664EPHA8_HUMAN54-2752220--
1.4ENST000001662444ENSE00000759543chr1:22912973-22913128156EPHA8_HUMAN275-327530--
1.5aENST000001662445aENSE00001131796chr1:22915364-22915699336EPHA8_HUMAN327-4391130--
1.6ENST000001662446ENSE00000759532chr1:22919819-22919943125EPHA8_HUMAN439-480420--
1.7ENST000001662447ENSE00000759516chr1:22920017-22920179163EPHA8_HUMAN481-535550--
1.8ENST000001662448ENSE00000759515chr1:22921723-2292181694EPHA8_HUMAN535-566320--
1.9ENST000001662449ENSE00000759471chr1:22922599-2292266668EPHA8_HUMAN566-589240--
1.10ENST0000016624410ENSE00000560716chr1:22923805-22923969165EPHA8_HUMAN589-644562A:627-644
B:627-644
18
18
1.11ENST0000016624411ENSE00000388463chr1:22924169-22924354186EPHA8_HUMAN644-706632A:644-706
B:644-706
63
63
1.12ENST0000016624412ENSE00000560718chr1:22924644-2292470562EPHA8_HUMAN706-726212A:706-726
B:706-726
21
21
1.13ENST0000016624413ENSE00000388465chr1:22925331-22925540210EPHA8_HUMAN727-796702A:727-796 (gaps)
B:727-795
70
69
1.14ENST0000016624414ENSE00001753689chr1:22927154-22927303150EPHA8_HUMAN797-846502A:800-846
B:797-846
47
50
1.15ENST0000016624415ENSE00000859688chr1:22927391-22927581191EPHA8_HUMAN847-910642A:847-900
B:847-899
54
53
1.16ENST0000016624416ENSE00000388468chr1:22927793-22927966174EPHA8_HUMAN910-968590--
1.17ENST0000016624417ENSE00001156943chr1:22928120-229300871968EPHA8_HUMAN968-1005380--

(-) 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:267
 aligned with EPHA8_HUMAN | P29322 from UniProtKB/Swiss-Prot  Length:1005

    Alignment length:274
                                   636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896    
          EPHA8_HUMAN   627 TREIEASRIHIEKIIGSGDSGEVCYGRLRVPGQRDVPVAIKALKAGYTERQRRDFLSEASIMGQFDHPNIIRLEGVVTRGRLAMIVTEYMENGSLDTFLRTHDGQFTIMQLVGMLRGVGAGMRYLSDLGYVHRDLAARNVLVDSNLVCKVSDFGLSRVLEDDPDAAYTTTGGKIPIRWTAPEAIAFRTFSSASDVWSFGVVMWEVLAYGERPYWNMTNRDVISSVEEGYRLPAPMGCPHALHQLMLDCWHKDRAQRPRFSQIVSVLDALIRSPE 900
               SCOP domains d3kula_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3kulA01 A:627-715 Phosphorylase Kinase; domain 1                                         3kulA02 A:716-900 Transferase(Phosphotransferase) domain 1                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee...eeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhh.........eeeeehhhhh.eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..----..ee..---.hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L---------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10         -------------------------------------------------------------Exon 1.12            Exon 1.13  PDB: A:727-796 (gaps) UniProt: 727-796                     Exon 1.14  PDB: A:800-846 UniProt: 797-846        Exon 1.15  PDB: A:847-900 UniProt: 847-910             Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.11  PDB: A:644-706 UniProt: 644-706                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kul A 627 TREIEASRIHIEKIIGSGDSGEVCYGRLRVPGQRDVPVAIKALKAGYTERQRRDFLSEASIMGQFDHPNIIRLEGVVTRGRLAMIVTEYMENGSLDTFLRTHDGQFTIMQLVGMLRGVGAGMRYLSDLGYVHRDLAARNVLVDSNLVCKVSDFGLSRVLE----AAYTTT---IPIRWTAPEAIAFRTFSSASDVWSFGVVMWEVLAYGERPYWNMTNRDVISSVEEGYRLPAPMGCPHALHQLMLDCWHKDRAQRPRFSQIVSVLDALIRSPE 900
                                   636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786    |  796   |   806       816       826       836       846       856       866       876       886       896    
                                                                                                                                                                                         786  791  796 800                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with EPHA8_HUMAN | P29322 from UniProtKB/Swiss-Prot  Length:1005

    Alignment length:273
                                   636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896   
          EPHA8_HUMAN   627 TREIEASRIHIEKIIGSGDSGEVCYGRLRVPGQRDVPVAIKALKAGYTERQRRDFLSEASIMGQFDHPNIIRLEGVVTRGRLAMIVTEYMENGSLDTFLRTHDGQFTIMQLVGMLRGVGAGMRYLSDLGYVHRDLAARNVLVDSNLVCKVSDFGLSRVLEDDPDAAYTTTGGKIPIRWTAPEAIAFRTFSSASDVWSFGVVMWEVLAYGERPYWNMTNRDVISSVEEGYRLPAPMGCPHALHQLMLDCWHKDRAQRPRFSQIVSVLDALIRSP 899
               SCOP domains d3kulb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3kulB01 B:627-715 Phosphorylase Kinase; domain 1                                         3kulB02 B:716-899 Transferase(Phosphotransferase) domain 1                                                                                                                               CATH domains
           Pfam domains (1) --------Pkinase_Tyr-3kulB01 B:635-892                                                                                                                                                                                                                                     ------- Pfam domains (1)
           Pfam domains (2) --------Pkinase_Tyr-3kulB02 B:635-892                                                                                                                                                                                                                                     ------- Pfam domains (2)
         Sec.struct. author ....hhh.eeeeeeeee...eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhhh.........eeeeehhhhh.eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........ee.-....hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10         -------------------------------------------------------------Exon 1.12            Exon 1.13  PDB: B:727-795 UniProt: 727-796 [INCOMPLETE]               Exon 1.14  PDB: B:797-846 UniProt: 797-846        Exon 1.15  PDB: B:847-899 UniProt: 847-910            Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.11  PDB: B:644-706 UniProt: 644-706                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kul B 627 TREIEASRIHIEKIIGSGDSGEVCYGRLRVPGQRDVPVAIKALKAGYTERQRRDFLSEASIMGQFDHPNIIRLEGVVTRGRLAMIVTEYMENGSLDTFLRTHDGQFTIMQLVGMLRGVGAGMRYLSDLGYVHRDLAARNVLVDSNLVCKVSDFGLSRVLEDDPDAAyTT-GGKIPIRWTAPEAIAFRTFSSASDVWSFGVVMWEVLAYGERPYWNMTNRDVISSVEEGYRLPAPMGCPHALHQLMLDCWHKDRAQRPRFSQIVSVLDALIRSP 899
                                   636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786      | |-|      806       816       826       836       846       856       866       876       886       896   
                                                                                                                                                                                                793-PTR                                                                                                      
                                                                                                                                                                                                  795 |                                                                                                      
                                                                                                                                                                                                    797                                                                                                      

   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EPHA8_HUMAN | P29322)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005004    GPI-linked ephrin receptor activity    Combining with a GPI-anchored ephrin to initiate a change in cell activity.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
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.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0033628    regulation of cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0006929    substrate-dependent cell migration    The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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