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 :  STRUCTURE OF THE HUMAN SMOOTHENED 7TM RECEPTOR IN COMPLEX WITH AN ANTITUMOR AGENT
 
Authors :  C. Wang, H. Wu, V. Katritch, G. W. Han, X. Huang, W. Liu, F. Y. Siu, B. L. Rot V. Cherezov, R. C. Stevens, Gpcr Network (Gpcr)
Date :  11 Mar 13  (Deposition) - 24 Apr 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Smoothened Receptor, Antitumor Agent, Novel Protein Engineering, Gpcr Network, Membrane Protein, Psi-Biology, Structural Genomics, Gpcr, Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wang, H. Wu, V. Katritch, G. W. Han, X. P. Huang, W. Liu, F. Y. Siu, B. L. Roth, V. Cherezov, R. C. Stevens
Structure Of The Human Smoothened Receptor Bound To An Antitumour Agent.
Nature V. 497 338 2013
PubMed-ID: 23636324  |  Reference-DOI: 10.1038/NATURE12167

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562, SMOOTHENED HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Fragment: BRIL
    Gene: CYBC, SMO_HUMAN, SMO, SMOH
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 562, 9606
    Synonym: CYTOCHROME B-562, SMO, PROTEIN GX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
11KS2Ligand/Ion4-FLUORO-N-METHYL-N-{1-[4-(1-METHYL-1H-PYRAZOL-5-YL)PHTHALAZIN-1-YL]PIPERIDIN-4-YL}-2-(TRIFLUOROMETHYL)BENZAMIDE
2OLA3Ligand/IonOLEIC ACID
3OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:219 , LEU A:221 , TRP A:281 , ASP A:384 , VAL A:386 , SER A:387 , PHE A:391 , TYR A:394 , LYS A:395 , ARG A:400 , GLN A:477 , TRP A:480 , GLU A:481 , PRO A:513 , GLU A:518 , ASN A:521 , LEU A:522BINDING SITE FOR RESIDUE 1KS A 601
02AC2SOFTWAREGLU A:447 , ARG A:451 , THR A:534BINDING SITE FOR RESIDUE OLC A 602
03AC3SOFTWARETYR A:397 , ARG A:398 , ALA A:401 , ALA A:406 , PHE A:474 , ALA B:377BINDING SITE FOR RESIDUE OLC A 603
04AC4SOFTWARESER A:468 , TYR A:472 , PHE A:475 , ASN A:476BINDING SITE FOR RESIDUE OLC A 604
05AC5SOFTWAREGLY A:288 , ILE A:316BINDING SITE FOR RESIDUE OLA A 605
06AC6SOFTWARETYR A:323 , HIS A:361 , TRP A:365BINDING SITE FOR RESIDUE OLA A 606
07AC7SOFTWAREPRO A:220 , LEU A:221BINDING SITE FOR RESIDUE PEG A 607
08AC8SOFTWAREGLN A:380 , ASN A:396 , TYR A:399 , HOH A:714 , ASN B:396 , TYR B:399BINDING SITE FOR RESIDUE PGE A 608
09AC9SOFTWAREASP A:229 , TYR A:233 , LYS A:519BINDING SITE FOR RESIDUE PG4 A 609
10BC1SOFTWAREASN B:219 , LEU B:221 , MET B:230 , TRP B:281 , MET B:301 , ASP B:384 , VAL B:386 , SER B:387 , PHE B:391 , TYR B:394 , LYS B:395 , ARG B:400 , GLN B:477 , TRP B:480 , GLU B:481 , PRO B:513 , GLU B:518 , ASN B:521 , LEU B:522BINDING SITE FOR RESIDUE 1KS B 601
11BC2SOFTWAREASP B:287 , GLU B:292 , ILE B:293BINDING SITE FOR RESIDUE OLC B 602
12BC3SOFTWARETYR B:233 , LYS B:519BINDING SITE FOR RESIDUE OLC B 603
13BC4SOFTWAREILE B:413 , TYR B:417BINDING SITE FOR RESIDUE OLA B 604
14BC5SOFTWARETHR B:311 , LEU B:312 , SER B:313 , HOH B:759BINDING SITE FOR RESIDUE PEG B 605

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:193 -A:213
2A:217 -A:295
3A:314 -A:390
4A:490 -A:507
5B:193 -B:213
6B:217 -B:295
7B:314 -B:390
8B:490 -B:507

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Val A:195 -Pro A:196
2Tyr A:262 -Pro A:263
3Glu A:305 -Pro A:306
4Val B:195 -Pro B:196
5Tyr B:262 -Pro B:263
6Glu B:305 -Pro B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JKV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JKV)

(-) Exons   (0, 0)

(no "Exon" information available for 4JKV)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...........eee..hhh.ee..eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jkv A  -1 GTADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGTTYQPGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSIKSNHPGLLSEKAASKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQANCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWC 550
                                     8        18        28        38        48        58        68        78        88        98       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351||     363       373       383       393       403       413       423       433       443       453       463       473       483       493|      516       526       536       546    
                                                                                                                                     106|                                                                                                                                                               352|                                                                                                                                       493|                                           
                                                                                                                                      190                                                                                                                                                                355                                                                                                                                        507                                           


Chain B from PDB  Type:PROTEIN  Length:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......eee..hhhhh......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jkv B   0 TADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSIKSNHPGLLSEKAASKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQANDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWCRL 552
                                     9        19        29        39        49        59        69        79        89        99      |192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342   ||  360       370       380       390       400       410       420       430       440       450       460       470       480       490  ||   512       522       532       542       552
                                                                                                                                    106|                                                                                                                                                         346|                                                                                                                                       493|                                              
                                                                                                                                     190                                                                                                                                                          355                                                                                                                                        506
   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 4JKV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JKV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JKV)

(-) Gene Ontology  (107, 107)

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
    1KS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:305 - Pro A:306   [ RasMol ]  
    Glu B:305 - Pro B:306   [ RasMol ]  
    Tyr A:262 - Pro A:263   [ RasMol ]  
    Tyr B:262 - Pro B:263   [ RasMol ]  
    Val A:195 - Pro A:196   [ RasMol ]  
    Val B:195 - Pro B:196   [ 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
  4jkv
    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
  C562_ECOLX | P0ABE7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SMO_HUMAN | Q99835
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  C562_ECOLX | P0ABE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SMO_HUMAN | Q99835
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi
        SMO_HUMAN | Q99835: 4n4w 4o9r 4qim 4qin 5l7d 5l7i 5v56 5v57

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JKV)