Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MONKEY TLR7 IN COMPLEX WITH LOXORIBINE AND POLYU
 
Authors :  Z. Zhang, U. Ohto, T. Shimizu
Date :  14 Jul 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Immune System, Tlr7, Innate Immunity, Ssrna Recogniton, Immune System-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, U. Ohto, T. Shibata, E. Krayukhina, M. Taoka, Y. Yamauchi, H. Tanji, T. Isobe, S. Uchiyama, K. Miyake, T. Shimizu
Structural Analysis Reveals That Toll-Like Receptor 7 Is A Dual Receptor For Guanosine And Single-Stranded Rna
Immunity V. 45 737 2016
PubMed-ID: 27742543  |  Reference-DOI: 10.1016/J.IMMUNI.2016.09.011

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 7
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Plasmid: PMT/BIP/V5-HIS
    Expression System Taxid: 7215
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 27-839
    Gene: TLR7
    Mutation: YES
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
    Synonym: UNCHARACTERIZED PROTEIN
 
Molecule 2 - RNA (5'-R(P*UP*UP*UP*U)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
3SDL2Ligand/Ion2-AZANYL-9-[(2~{R},3~{R},4~{S},5~{R})-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]-7-PROP-2-ENYL-1~{H}-PURINE-6,8-DIONE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:532 , ASP A:555 , LEU A:557 , GLY A:584 , ILE A:585 , THR A:586 , PHE B:351 , GLN B:354 , TYR B:356 , VAL B:381 , PHE B:408 , LYS B:432binding site for residue SDL B 901
02AC2SOFTWAREPHE A:351 , GLN A:354 , TYR A:356 , VAL A:381 , PHE A:408 , LYS A:432 , THR B:532 , ASP B:555 , LEU B:557 , GLY B:584 , ILE B:585 , THR B:586binding site for residue SDL B 902
03AC3SOFTWAREARG B:696 , ASN B:720binding site for residue PO4 B 908
04AC4SOFTWAREASN A:69 , VAL A:92 , GLU A:93 , SER A:131binding site for Mono-Saccharide NAG A 901 bound to ASN A 69
05AC5SOFTWARECYS A:183 , TYR A:184 , PRO A:188 , CYS A:189 , TYR A:190 , VAL A:191 , SER A:192 , ASN A:215binding site for Poly-Saccharide residues NAG A 902 through NAG A 903 bound to ASN A 215
06AC6SOFTWARESER A:490 , CYS A:491 , SER A:501 , LYS A:502 , ASN A:523 , TYR A:546 , ASP A:548binding site for Mono-Saccharide NAG A 905 bound to ASN A 523
07AC7SOFTWAREGLU A:654 , ASP A:656 , ASN A:679 , HOH A:1009binding site for Mono-Saccharide NAG A 904 bound to ASN A 679
08AC8SOFTWAREASN B:69 , GLU B:93 , SER B:131binding site for Mono-Saccharide NAG B 907 bound to ASN B 69
09AC9SOFTWARECYS B:183 , TYR B:184 , PRO B:188 , CYS B:189 , TYR B:190 , VAL B:191 , SER B:192 , ASN B:215binding site for Poly-Saccharide residues NAG B 904 through NAG B 905 bound to ASN B 215
10AD1SOFTWARESER B:490 , CYS B:491 , SER B:501 , LYS B:502 , ASN B:523 , TYR B:546 , ASP B:548binding site for Mono-Saccharide NAG B 906 bound to ASN B 523
11AD2SOFTWARESER B:559 , ASN B:590 , THR B:612 , SER B:613binding site for Mono-Saccharide NAG B 903 bound to ASN B 590

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:51
2A:98 -A:475
3A:100 -A:112
4A:183 -A:189
5A:260 -A:273
6A:263 -A:270
7A:491 -A:521
8A:787 -A:814
9A:789 -A:833
10B:36 -B:51
11B:98 -B:475
12B:100 -B:112
13B:183 -B:189
14B:260 -B:273
15B:263 -B:270
16B:491 -B:521
17B:787 -B:814
18B:789 -B:833

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Pro A:31 -Lys A:32
2Thr A:221 -Val A:222
3Gly A:816 -Pro A:817
4Thr B:221 -Val B:222
5Gly B:816 -Pro B:817

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GMG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GMG)

(-) Exons   (0, 0)

(no "Exon" information available for 5GMG)

(-) 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:762
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee.....eee..................eee.......eehhhhhh......eee.....................ee............eee..................eee.......ee....hhhhh...eee...............ee............eee..................eee.....................eee.................hhhhh................eee.........hhhhhh......eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhhh...eee.......................hhhhh.eee.........hhhhhh......eee......................eee.....................eee....hhhhhh.................eee....................eee....hhhhhh..................eee......................eee.........hhhhhhhh....eee...........hhhhh.....eee.....................eee..............hhhhhh...eee.....ee.hhhhhhhhhhhhhh............eeehhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gmg A  28 RWFPKTLPCDVTLDHVIVDCTDKHLTEIPGGIPTNTTNLTLTINHIPDISPASFHRLVHLVEIDFRCNCVPIRLGSKSNMCPRRLQIKPRSFSGLTYLKSLYLDGNQLLEIPQGLPPSLQLLSLEANNIFSIRKEQLTELANIEILYLGQNCYYRNPCYVSYSIEKDAFLNLTKLKVLSLKDNNVTTVPTVLPSTLTELYLYNNMIAEIQEDDFNNLNQLQILDLSGNCPRCYNAPFPCTPCKNNSPLQIPVNAFDALTELKVLRLHSNSLQHVPPRWFKNINNLQELDLSQNFLAKEIGDAKFLHFLPNLIQLDLSFNFELQVYRASMNLSQAFSSLKSLKILRIRGYVFKELKSFQLSPLHNLQNLEVLDLGTNFIKIANLSMFKQFKRLKVIDLSVNKISPLYYFRYDKYARSCRSCYKYGQTLDLSKNSIFFIKSSDFQHLSFLKCLNLSGNLISQTLNGSEFQPLAELRYLDFSNNRLDLLHSTAFEELRKLEVLDISSNSHYFQSEGITHMLNFTKNLKVLQKLMMNDNDISSSTSRTMESESLRTLEFRGNHLDVLWRDGDNRYLQLFKNLLKLEELDISKNSLSFLPSGVFDGMPPNLKNLSLAKNGLKSFIWEKLRYLKNLETLDLSHNQLTTVPERLSNCSRSLKNLILKNNQIRSLTKYFLQDAFQLRYLDLSSNKIQMIQKTSFPENVLNNLKMLLLHHNRFLCTCDAVWFVWWVQHTEVTIPYLATDVTCVGPGAHKGQSVISLDLYTC 833
                                    37   ||   51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431   ||  468       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831  
                                        41|                                                                                                                                                                                                                                                                                                                                                                                                  435|          476|                                                                                                                                                                                                                                                                                                                                                       
                                         46                                                                                                                                                                                                                                                                                                                                                                                                   463           490                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:762
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee.....eee..................eee.......eehhhhhh......eee.....................ee............eee..................eee.......ee....hhhhh...eee...............ee............eee..................eee.....................eee.................hhhhh................eee.........hhhhhh......eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhhh...eee.......................hhhhh.eee.........hhhhhh......eee......................eee.....................eee....hhhhhh.................eee....................eee....hhhhhh..................eee......................eee.........hhhhhhhh....eee...........hhhhh.....eee.....................eee..............hhhhhh...eee.....ee.hhhhhhhhhhhhhh............eeehhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gmg B  28 RWFPKTLPCDVTLDHVIVDCTDKHLTEIPGGIPTNTTNLTLTINHIPDISPASFHRLVHLVEIDFRCNCVPIRLGSKSNMCPRRLQIKPRSFSGLTYLKSLYLDGNQLLEIPQGLPPSLQLLSLEANNIFSIRKEQLTELANIEILYLGQNCYYRNPCYVSYSIEKDAFLNLTKLKVLSLKDNNVTTVPTVLPSTLTELYLYNNMIAEIQEDDFNNLNQLQILDLSGNCPRCYNAPFPCTPCKNNSPLQIPVNAFDALTELKVLRLHSNSLQHVPPRWFKNINNLQELDLSQNFLAKEIGDAKFLHFLPNLIQLDLSFNFELQVYRASMNLSQAFSSLKSLKILRIRGYVFKELKSFQLSPLHNLQNLEVLDLGTNFIKIANLSMFKQFKRLKVIDLSVNKISPLYYFRYDKYARSCRSCYKYGQTLDLSKNSIFFIKSSDFQHLSFLKCLNLSGNLISQTLNGSEFQPLAELRYLDFSNNRLDLLHSTAFEELRKLEVLDISSNSHYFQSEGITHMLNFTKNLKVLQKLMMNDNDISSSTSRTMESESLRTLEFRGNHLDVLWRDGDNRYLQLFKNLLKLEELDISKNSLSFLPSGVFDGMPPNLKNLSLAKNGLKSFIWEKLRYLKNLETLDLSHNQLTTVPERLSNCSRSLKNLILKNNQIRSLTKYFLQDAFQLRYLDLSSNKIQMIQKTSFPENVLNNLKMLLLHHNRFLCTCDAVWFVWWVQHTEVTIPYLATDVTCVGPGAHKGQSVISLDLYTC 833
                                    37   ||   51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431   ||  468       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831  
                                        41|                                                                                                                                                                                                                                                                                                                                                                                                  435|          476|                                                                                                                                                                                                                                                                                                                                                       
                                         46                                                                                                                                                                                                                                                                                                                                                                                                   463           490                                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:DNA/RNA  Length:4
                                    
                 5gmg C   1 UUUU   4


Chain D from PDB  Type:DNA/RNA  Length:4
                                    
                 5gmg D   1 UUUU   4
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GMG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GMG)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SDL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:816 - Pro A:817   [ RasMol ]  
    Gly B:816 - Pro B:817   [ RasMol ]  
    Pro A:31 - Lys A:32   [ RasMol ]  
    Thr A:221 - Val A:222   [ RasMol ]  
    Thr B:221 - Val B:222   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5gmg
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B3Y653_MACMU | B3Y653
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  B3Y653_MACMU | B3Y653
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3Y653_MACMU | B3Y653: 5gmf 5gmh

(-) Related Entries Specified in the PDB File

5gmf 5gmh