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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-5 IN COMPLEX WITH ITS ALPHA RECEPTOR
 
Authors :  S. Kusano, M. Kukimoto-Niino, M. Shirouzu, S. Yokoyama
Date :  28 Dec 11  (Deposition) - 25 Jul 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cytokine, Eosinophilic, Asthma, Jak/Stat, Fibronectin Iii-Like (Fn Iii) Domain, Canonical Cytokine Receptor Homology Module (Crm), B Cell Growth, Ig Secretion, Eosinophils Proliferation, Cell Surface, Cytokine-Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kusano, M. Kukimoto-Niino, N. Hino, N. Ohsawa, M. Ikutani, S. Takaki, K. Sakamoto, M. Hara-Yokoyama, M. Shirouzu, K. Takatsu, S. Yokoyama
Structural Basis Of Interleukin-5 Dimer Recognition By Its Alpha Receptor
Protein Sci. V. 21 850 2012
PubMed-ID: 22528658  |  Reference-DOI: 10.1002/PRO.2072

(-) Compounds

Molecule 1 - INTERLEUKIN-5
    ChainsA, B
    EngineeredYES
    Expression SystemCELL-FREE SYNTHESIS
    FragmentUNP RESIDUES 23-134
    GeneIL5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-5, B-CELL DIFFERENTIATION FACTOR I, EOSINOPHIL DIFFERENTIATION FACTOR, T-CELL REPLACING FACTOR, TRF
 
Molecule 2 - INTERLEUKIN-5 RECEPTOR SUBUNIT ALPHA
    ChainsC
    EngineeredYES
    Expression SystemCELL-FREE SYNTHESIS
    FragmentECTODOMAIN, UNP RESIDUES 21-335
    GeneIL5RA, IL5R
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-5 RECEPTOR SUBUNIT ALPHA, IL-5R SUBUNIT ALPHA, IL-5R- ALPHA, IL-5RA, CDW125

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VA2)

(-) Sites  (0, 0)

(no "Site" information available for 3VA2)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:63 -B:105
2A:105 -B:63
3C:134 -C:155
4C:182 -C:196
5C:269 -C:316

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val B:112 -Asn B:113
2Ala C:71 -Pro C:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020654I129VIL5RA_HUMANPolymorphism2290610CI129V
2UniProtVAR_020655V262AIL5RA_HUMANPolymorphism17879690CV262A

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.IL5RA_HUMAN32-123
241-334
  2C:32-123
C:241-333
2HEMATOPO_REC_S_F2PS01356 Short hematopoietin receptor family 2 signature.IL5RA_HUMAN153-182  1C:153-182

(-) Exons   (12, 16)

Asymmetric/Biological Unit (12, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002314542bENSE00000854388chr5:131879214-131879027188IL5_HUMAN1-48482A:24-48
B:24-48
25
25
1.2cENST000002314542cENSE00000763102chr5:131878818-13187878633IL5_HUMAN49-59112A:49-59
B:49-59
11
11
1.3bENST000002314543bENSE00000763103chr5:131877835-131877707129IL5_HUMAN60-102432A:60-102
B:60-102
43
43
1.4ENST000002314544ENSE00000854387chr5:131877601-131877136466IL5_HUMAN103-134322A:103-130
B:103-132
28
30

2.2fENST000002564522fENSE00001898297chr3:3151664-315162936IL5RA_HUMAN-00--
2.3bENST000002564523bENSE00000997127chr3:3150375-3150234142IL5RA_HUMAN-00--
2.4ENST000002564524ENSE00001322495chr3:3147220-314715269IL5RA_HUMAN-00--
2.5ENST000002564525ENSE00002175535chr3:3146671-314658785IL5RA_HUMAN1-28281C:27-282
2.6ENST000002564526ENSE00001624596chr3:3144504-3144359146IL5RA_HUMAN28-76491C:28-7649
2.7bENST000002564527bENSE00001730405chr3:3143514-3143376139IL5RA_HUMAN77-123471C:77-12347
2.8ENST000002564528ENSE00001634426chr3:3139974-3139821154IL5RA_HUMAN123-174521C:123-17452
2.9bENST000002564529bENSE00001733184chr3:3139741-3139554188IL5RA_HUMAN174-237641C:174-23764
2.10ENST0000025645210ENSE00001619473chr3:3137128-3136983146IL5RA_HUMAN237-285491C:237-28549
2.11aENST0000025645211aENSE00001657506chr3:3134046-3133908139IL5RA_HUMAN286-332471C:286-33247
2.13ENST0000025645213ENSE00000912359chr3:3118311-311821597IL5RA_HUMAN332-364331C:332-3332
2.14ENST0000025645214ENSE00000912357chr3:3116550-311646685IL5RA_HUMAN364-392290--
2.16aENST0000025645216aENSE00001908764chr3:3111995-3111421575IL5RA_HUMAN393-420280--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:107
 aligned with IL5_HUMAN | P05113 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:107
                                    33        43        53        63        73        83        93       103       113       123       
            IL5_HUMAN    24 IPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEW 130
               SCOP domains d3va2a_ A: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: A:24-48  Exon 1.2c  Exon 1.3b  PDB: A:60-102 UniProt: 60-102   Exon 1.4  PDB: A:103-130     Transcript 1
                 3va2 A  24 IPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEW 130
                                    33        43        53        63        73        83        93       103       113       123       

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with IL5_HUMAN | P05113 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:109
                                    33        43        53        63        73        83        93       103       113       123         
            IL5_HUMAN    24 IPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWII 132
               SCOP domains d3va2b_ B: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.hhhhhh......ee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: B:24-48  Exon 1.2c  Exon 1.3b  PDB: B:60-102 UniProt: 60-102   Exon 1.4  PDB: B:103-132       Transcript 1
                 3va2 B  24 IPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWII 132
                                    33        43        53        63        73        83        93       103       113       123         

Chain C from PDB  Type:PROTEIN  Length:307
 aligned with IL5RA_HUMAN | Q01344 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:307
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       
          IL5RA_HUMAN    27 KISLLPPVNFTIKVTGLAQVLLQWKPNPDQEQRNVNLEYQVKINAPKEDDYETRITESKCVTILHKGFSASVRTILQNDHSLLASSWASAELHAPPGSPGTSIVNLTCTTNTTEDNYSRLRSYQVSLHCTWLVGTDAPEDTQYFLYYRYGSWTEECQEYSKDTLGRNIACWFPRTFILSKGRDWLAVLVNGSSKHSAIRPFDQLFALHAIDQINPPLNVTAEIEGTRLSIQWEKPVSAFPIHCFDYEVKIHNTRNGYLQIEKLMTNAFISIIDDLSKYDVQVRAAVSSMCREAGLWSEWSQPIYVGN 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..eeeeeee............eeeeeeee...eeeee...eeeee......eeeeeeeeee....eee...eeeee.....hhhhh.eeeeeeeeee..........eeeeeeeee.........eeeeeeee..eeee...eee.....eeeeee...........eeeeeeeee........eeeeeehhhhee....eeeeeeee..eeeeeee..........eeeeeeeee.....eeeeee...eeeee.....eeeeeeeeee................eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FN3  PDB: C:32-123 UniProt: 32-123                                                          -----------------------------HEMATOPO_REC_S_F2             ----------------------------------------------------------FN3  PDB: C:241-333 UniProt: 241-334                                                          PROSITE
           Transcript 2 (1) 2.------------------------------------------------Exon 2.7b  PDB: C:77-123 UniProt: 77-123       -----------------------------------------------------------------------------------------------------------------Exon 2.10  PDB: C:237-285 UniProt: 237-285       Exon 2.11a  PDB: C:286-332 UniProt: 286-332    - Transcript 2 (1)
           Transcript 2 (2) -Exon 2.6  PDB: C:28-76 UniProt: 28-76            ----------------------------------------------Exon 2.8  PDB: C:123-174 UniProt: 123-174           -------------------------------------------------------------------------------------------------------------------------------------------------------------2. Transcript 2 (2)
           Transcript 2 (3) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.9b  PDB: C:174-237 UniProt: 174-237                      ------------------------------------------------------------------------------------------------ Transcript 2 (3)
                 3va2 C  27 KISLLPPVNFTIKVTGLAQVLLQWKPNPDQEQRNVNLEYQVKINAPKEDDYETRITESKCVTILHKGFSASVRTILQNDHSLLASSWASAELHAPPGSPGTSIVNLTCTTNTTEDNYSRLRSYQVSLHCTWLVGTDAPEDTQYFLYYRYGSWTEECQEYSKDTLGRNIACWFPRTFILSKGRDWLAVLVNGSSKHSAIRPFDQLFALHAIDQINPPLNVTAEIEGTRLSIQWEKPVSAFPIHCFDYEVKIHNTRNGYLQIEKLMTNAFISIIDDLSKYDVQVRAAVSSMCREAGLWSEWSQPIYVGN 333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VA2)

(-) Gene Ontology  (35, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IL5_HUMAN | P05113)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0005137    interleukin-5 receptor binding    Interacting selectively and non-covalently with the interleukin-5 receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0046427    positive regulation of JAK-STAT cascade    Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045645    positive regulation of eosinophil differentiation    Any process that activates or increases the frequency, rate or extent of eosinophil differentiation.
    GO:0051024    positive regulation of immunoglobulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0071803    positive regulation of podosome assembly    Any process that activates or increases the rate or extent of podosome assembly.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

Chain C   (IL5RA_HUMAN | Q01344)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0004896    cytokine receptor activity    Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0004914    interleukin-5 receptor activity    Combining with interleukin-5 and transmitting the signal from one side of the membrane to the other to initiate a change in cell 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).
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071310    cellular response to organic substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    GO:0038043    interleukin-5-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-5 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032674    regulation of interleukin-5 production    Any process that modulates the frequency, rate, or extent of interleukin-5 production.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL5RA_HUMAN | Q013441obx 1obz 3qt2
        IL5_HUMAN | P051131hul 3qt2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VA2)