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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOMEGALOVIRUS IL-10 BOUND TO SOLUBLE HUMAN IL-10R1
 
Authors :  B. C. Jones, N. J. Logsdon, K. Josephson, J. Cook, P. A. Barry, M. R. Walte
Date :  13 May 02  (Deposition) - 17 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  L,M,R,S
Keywords :  Interleukin 10, Helix Bundle, Receptor Complex, Molecular Recognition, Structure Mimic, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. C. Jones, N. J. Logsdon, K. Josephson, J. Cook, P. A. Barry, M. R. Walter
Crystal Structure Of Human Cytomegalovirus Il-10 Bound To Soluble Human Il-10R1.
Proc. Natl. Acad. Sci. Usa V. 99 9404 2002
PubMed-ID: 12093920  |  Reference-DOI: 10.1073/PNAS.152147499

(-) Compounds

Molecule 1 - INTERLEUKIN-10 RECEPTOR ALPHA CHAIN
    ChainsR, S
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System PlasmidPMTV5HIS
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 22-235
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-10R-A, IL-10R1
 
Molecule 2 - INTERLEUKIN-10-LIKE PROTEIN
    ChainsL, M
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System PlasmidPMTV5HIS
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    FragmentRESIDUES 20-176
    Organism CommonHUMAN CYTOMEGALOVIRUS
    Organism ScientificHUMAN HERPESVIRUS 5
    Organism Taxid10359

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit LMRS

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN L:134BINDING SITE FOR RESIDUE NAG L 201
2AC2SOFTWAREGLU M:129 , ASN M:134BINDING SITE FOR RESIDUE NAG M 202

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1L:12 -L:108
2L:59 -M:59
3L:62 -L:114
4M:12 -M:108
5M:62 -M:114
6R:35 -R:54
7R:181 -R:202
8S:35 -S:54
9S:181 -S:202

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LQS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 22)

Asymmetric/Biological Unit (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_016294L61VI10R1_HUMANPolymorphism4252250R/SL40V
02UniProtVAR_071663W69RI10R1_HUMANDisease (IBD28)  ---R/SW48R
03UniProtVAR_063542T84II10R1_HUMANDisease (IBD28)137853580R/ST63I
04UniProtVAR_071664Y91CI10R1_HUMANDisease (IBD28)  ---R/SY70C
05UniProtVAR_071665R101WI10R1_HUMANDisease (IBD28)368287711R/SR80W
06UniProtVAR_016295V113II10R1_HUMANPolymorphism4252303R/SV92I
07UniProtVAR_071666R117HI10R1_HUMANDisease (IBD28)199989396R/SR96H
08UniProtVAR_063543G141RI10R1_HUMANDisease (IBD28)137853579R/SG120R
09UniProtVAR_016296S159GI10R1_HUMANPolymorphism3135932R/SS138G
10UniProtVAR_016297R212QI10R1_HUMANPolymorphism4252273R/SR191Q
11UniProtVAR_020004I224VI10R1_HUMANPolymorphism2228055R/SI203V

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_10PS00520 Interleukin-10 family signature.IL10H_HCMVA76-96
 
  2L:57-77
M:57-77

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002277521aENSE00002150184chr11:117857063-117857249187I10R1_HUMAN1-23232R:2-2
S:2-2
1
1
1.1iENST000002277521iENSE00001053160chr11:117859097-117859217121I10R1_HUMAN23-63412R:2-42
S:2-42
41
41
1.2bENST000002277522bENSE00000795930chr11:117860157-117860335179I10R1_HUMAN63-123612R:42-102
S:42-102
61
61
1.3cENST000002277523cENSE00001053158chr11:117863956-117864125170I10R1_HUMAN123-179572R:102-158
S:102-158
57
57
1.4aENST000002277524aENSE00001053155chr11:117864714-117864864151I10R1_HUMAN180-230512R:159-208
S:159-207
50
49
1.5bENST000002277525bENSE00001053157chr11:117866304-117866425122I10R1_HUMAN230-270410--
1.6gENST000002277526gENSE00002200423chr11:117869430-1178721942765I10R1_HUMAN271-5783080--

(-) 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 L from PDB  Type:PROTEIN  Length:142
 aligned with IL10H_HCMVA | P17150 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:142
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172  
          IL10H_HCMVA    33 TKPQCRPEDYATRLQDLRVTFHRVKPTLQREDDYSVWLDGTVVKGCWGCSVMDWLLRRYLEIVFPAGDHVYPGLKTELHSMRSTLESIYKDMRQCPLLGCGDKSVISRLSQEAERKSDNGTRKGLSELDTLFSRLEEYLHSR 174
               SCOP domains d1lqsl_ L: Interleukin-10 (cytokine synthesis inhibitory factor, CSIF)                                                                         SCOP domains
               CATH domains 1lqsL01 L:8-114  [code=1.20.1250.10, no name defined]                                               1lqsL02 L:116-157 Interleukin-10, domain 2 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------INTERLEUKIN_10       ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqs L   8 TKPQCRPEDYATRLQDLRVTFHRVKPTLQREDDYSVWLDGTVVKGCWGCSVMDWLLRRYLEIVFPAGDHVYPGLKTELHSMRSTLESIYKDMRQCPLLGCGDKSVISRLSQEAERKSDNGTRKGLSELDTLFSRLEEYLHSR 157
                                 || 19        29        40        50 ||     63        73        83        93       103       114|      125       135       145       155  
                                13|                    38|          52|                                                     112||                                         
                                 16                     40           56                                                      114|                                         
                                                                                                                              116                                         

Chain M from PDB  Type:PROTEIN  Length:142
 aligned with IL10H_HCMVA | P17150 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:142
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172  
          IL10H_HCMVA    33 TKPQCRPEDYATRLQDLRVTFHRVKPTLQREDDYSVWLDGTVVKGCWGCSVMDWLLRRYLEIVFPAGDHVYPGLKTELHSMRSTLESIYKDMRQCPLLGCGDKSVISRLSQEAERKSDNGTRKGLSELDTLFSRLEEYLHSR 174
               SCOP domains d1lqsm_ M: Interleukin-10 (cytokine synthesis inhibitory factor, CSIF)                                                                         SCOP domains
               CATH domains 1lqsM01 M:8-114  [code=1.20.1250.10, no name defined]                                               1lqsM02 M:116-157 Interleukin-10, domain 2 CATH domains
           Pfam domains (1) IL10-1lqsM01 M:8-156                                                                                                                         - Pfam domains (1)
           Pfam domains (2) IL10-1lqsM02 M:8-156                                                                                                                         - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------INTERLEUKIN_10       ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqs M   8 TKPQCRPEDYATRLQDLRVTFHRVKPTLQREDDYSVWLDGTVVKGCWGCSVMDWLLRRYLEIVFPAGDHVYPGLKTELHSMRSTLESIYKDMRQCPLLGCGDKSVISRLSQEAERKSDNGTRKGLSELDTLFSRLEEYLHSR 157
                                 || 19        29        40        50 ||     63        73        83        93       103       114|      125       135       145       155  
                                13|                    38|          52|                                                     112||                                         
                                 16                     40           56                                                      114|                                         
                                                                                                                              116                                         

Chain R from PDB  Type:PROTEIN  Length:207
 aligned with I10R1_HUMAN | Q13651 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:207
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       
          I10R1_HUMAN    23 GTELPSPPSVWFEAEFFHHILHWTPIPNQSESTCYEVALLRYGIESWNSISNCSQTLSYDLTAVTLDLYHSNGYRARVRAVDGSRHSNWTVTNTRFSVDEVTLTVGSVNLEIHNGFILGKIQLPRPKMAPANDTYESIFSHFREYEIAIRKVPGNFTFTHKKVKHENFSLLTSGEVGEFCVQVKPSVASRSNKGMWSKEECISLTRQ 229
               SCOP domains d1lqsr1 R:2-100 Interleukin-10 receptor 1, IL-10R1                                                 d1lqsr2 R:101-208 Interleukin-10 receptor 1, IL-10R1                                                         SCOP domains
               CATH domains 1lqsR01 R:2-103 Immunoglobulins                                                                       1lqsR02 R:104-206 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..eeeeee..........eeeeeeee.....eeeeeeee...eee.hhhh.hhhhh..eeeeeeeee..ee...ee.....hhh.ee....eeeeeee..eeeeeee...........hhhhhh...eeeeeeeee.......eeeee...eeeee......eeeeeeeeee............eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V-------R--------------I------C---------W-----------I---H-----------------------R-----------------G----------------------------------------------------Q-----------V----- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1---------------------------------------Exon 1.2b  PDB: R:42-102 UniProt: 63-123                     --------------------------------------------------------Exon 1.4a  PDB: R:159-208 UniProt: 180-230         Transcript 1 (1)
           Transcript 1 (2) Exon 1.1i  PDB: R:2-42 UniProt: 23-63    -----------------------------------------------------------Exon 1.3c  PDB: R:102-158 UniProt: 123-179               -------------------------------------------------- Transcript 1 (2)
                 1lqs R   2 GTELPSPPSVWFEAEFFHHILHWTPIPQQSESTCYEVALLRYGIESWNSISQCSQTLSYDLTAVTLDLYHSNGYRARVRAVDGSRHSQWTVTNTRFSVDEVTLTVGSVNLEIHNGFILGKIQLPRPKMAPAQDTYESIFSHFREYEIAIRKVPGQFTFTHKKVKHEQFSLLTSGEVGEFCVQVKPSVASRSNKGMWSKEECISLTRQ 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       

Chain S from PDB  Type:PROTEIN  Length:206
 aligned with I10R1_HUMAN | Q13651 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:206
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
          I10R1_HUMAN    23 GTELPSPPSVWFEAEFFHHILHWTPIPNQSESTCYEVALLRYGIESWNSISNCSQTLSYDLTAVTLDLYHSNGYRARVRAVDGSRHSNWTVTNTRFSVDEVTLTVGSVNLEIHNGFILGKIQLPRPKMAPANDTYESIFSHFREYEIAIRKVPGNFTFTHKKVKHENFSLLTSGEVGEFCVQVKPSVASRSNKGMWSKEECISLTR 228
               SCOP domains d1lqss1 S:2-100 Interleukin-10 receptor 1, IL-10R1                                                 d1lqss2 S:101-207 Interleukin-10 receptor 1, IL-10R1                                                        SCOP domains
               CATH domains 1lqsS01 S:2-103 Immunoglobulins                                                                       1lqsS02 S:104-206 Immunoglobulins                                                                      - CATH domains
           Pfam domains (1) Tissue_fac-1lqsS01 S:2-90                                                                --------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Tissue_fac-1lqsS02 S:2-90                                                                --------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .........eeeeee..eeeeee..........eeeeeeee......eeeeeee...eee.hhhhhhhhhh..eeeeeeeee..ee...ee.....hhh.ee....eeeeeee..eeeeeee...........hhhhhh...eeeeeeeee.......eeeee...eeeee......eeeeeeeeee............eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V-------R--------------I------C---------W-----------I---H-----------------------R-----------------G----------------------------------------------------Q-----------V---- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1---------------------------------------Exon 1.2b  PDB: S:42-102 UniProt: 63-123                     --------------------------------------------------------Exon 1.4a  PDB: S:159-207 UniProt: 180-230        Transcript 1 (1)
           Transcript 1 (2) Exon 1.1i  PDB: S:2-42 UniProt: 23-63    -----------------------------------------------------------Exon 1.3c  PDB: S:102-158 UniProt: 123-179               ------------------------------------------------- Transcript 1 (2)
                 1lqs S   2 GTELPSPPSVWFEAEFFHHILHWTPIPQQSESTCYEVALLRYGIESWNSISQCSQTLSYDLTAVTLDLYHSNGYRARVRAVDGSRHSQWTVTNTRFSVDEVTLTVGSVNLEIHNGFILGKIQLPRPKMAPAQDTYESIFSHFREYEIAIRKVPGQFTFTHKKVKHEQFSLLTSGEVGEFCVQVKPSVASRSNKGMWSKEECISLTR 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      

   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  (2, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L,M   (IL10H_HCMVA | P17150)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
biological process
    GO:0039673    evasion by virus of host dendritic cell activity    Any process by which a virus avoids the effects mediated by the host organism's dendritic cells.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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.

Chain R,S   (I10R1_HUMAN | Q13651)
molecular function
    GO:0019969    interleukin-10 binding    Interacting selectively and non-covalently with interleukin-10.
    GO:0004920    interleukin-10 receptor activity    Combining with interleukin-10 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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    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:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    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: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
        I10R1_HUMAN | Q136511j7v 1y6k 1y6m 1y6n 5ixi

(-) Related Entries Specified in the PDB File

1j7v HUMAN IL-10 / IL-10R1 COMPLEX