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 HUMAN CEREBLON IN COMPLEX WITH DDB1 AND LENALIDOMIDE
 
Authors :  P. P. Chamberlain, B. Pagarigan, S. Delker, B. Leon, M. Riley
Date :  09 Jul 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Dcaf, Dna Binding Protein-Ligase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. P. Chamberlain, M. Wang, M. Riley, S. Delker, G. Carmel, K. Miller, A. Lopez-Girona, B. Pagarigan, B. Leon, E. Rychak, L. Corral, A. Lopez-Girona, Y. Ren, M. Wang, M. Riley, S. Delker, T. Ito, A. Hideki T. Mori, H. Handa, T. Hakoshima, T. O. Daniel, K. Miller, B. E. Cathers, G. Carmel, B. Pagarigan, B. Leon, E. Rychak, L. Corral, Y. Ren
Structural Basis For Responsiveness To Thalidomide-Analog Drugs Defined By The Crystal Structure Of The Human Cereblon:Ddb1:Lenalidomide Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA DAMAGE-BINDING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: DDB1, XAP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DDB P127 SUBUNIT,DNA DAMAGE-BINDING PROTEIN A,DDBA,DAMAGE- SPECIFIC DNA-BINDING PROTEIN 1,HBV X-ASSOCIATED PROTEIN 1,XAP-1,UV- DAMAGED DNA-BINDING FACTOR,UV-DAMAGED DNA-BINDING PROTEIN 1,UV-DDB 1, XPE-BINDING FACTOR,XPE-BF,XERODERMA PIGMENTOSUM GROUP E-COMPLEMENTING PROTEIN,XPCE
 
Molecule 2 - PROTEIN CEREBLON
    Chains: C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: CRBN, AD-006
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1LVY1Ligand/IonS-LENALIDOMIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:323 , CYS C:326 , CYS C:391 , CYS C:394binding site for residue ZN C 501
2AC2SOFTWAREASN C:351 , PRO C:352 , HIS C:378 , SER C:379 , TRP C:380 , TRP C:386 , TRP C:400 , PHE C:402binding site for residue LVY C 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:18 -A:313

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:660 -Ser A:661
2Gln C:115 -Lys C:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4TZ4)

(-) 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:1070
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeee........eeeeee..eeeeee....eeeeeee....eeeeeee........eeeeee...eeeeeeee...eeeeeeeee.............eeee.....eeeee....eeeeee..........eeee.....eeeeee.......eeeeeeee..eeeeeeeeee....eeee............eeee.......eeee....eeeee..eeeee.hhhhh.....eeee......eeeee....eeeeeeee....eeeeeeeee...eeeeee....eeeeee....eeeeeee....eeeeeeee.....eeeeeee.....eeeeee.hhhh.eeeeeeee..eeeeeeee.....eeeee........eeeeee..eeeeeeee..eeeee..........eeeeeee...eeeeee...eeeee.....eeeee.........eeee...eeeeee..eeeeee.......eeee......eee........eeeee.....eeeee...............eeeeeeeee..eeeeeeee...eeeeee...........eee......eeeeee...eeeeee....eee.................eeeee.......eeeee...eeeeeee....eeeeeeee...eeeeeeee....eeeeeeeeeee...ee...hhhhh..eeee...eeeeeeeeeee.....eeeeee....eeeeeeeee........eeeeeeee..........eeeeeeeee..eeeeeeeeee...eeeeeee..eeeeee..eeeeeee.....eeeeeeee......eeeee..eeeee.....eeeeee......eeeeeee.....eeeeeeee..eeeeee...eeeeee........eeeeeee....eeeeee.....eeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhh..........eeehhhhhhhhhhhhhhhhhhh...ee....ee.hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4tz4 A    2 SYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTALRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQNVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNEQGSYVVAMETFTNLGPIVDMCVVDLEQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEVACLDITPLGLSPLCAIGLTDISARILKLPSFELHKEMLGGIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDKKVTLGTQPTVLRTFRSSTTNVFACSDRPTVIYSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTTALRPSASTQALSSSVSSEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDEERQHLQEVGLFHLGEFVNVFCHGSLVTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGKREATADDLIKVVEELTRIHWSHPQFE 1147
                                    11        21        31        41    ||  53        63        73        83        93|      106       116       126       136       146       156       166       176       186       196       206  ||   217       227       237       247       257       267       277       287|      305       315       325       335 ||    349       359       372       382       392       402       412    || 424       434       444       454       464       474       484       494       504       514       524       534||     546|      560|      571    || 582 ||    593       603       613       623 ||    634       645       655     ||666       676       686       696       706       716       726       736       750       760      |786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976   ||  992      1002      1012||    1032      1042      1052      1062      1072     |1084      1094      1104      1114  ||  1127      1137      1147
                                                                       46|                                          93|                                                                                                             209|                                                                         287|                                      337|                       368|                                          417|                                                                                                                535|     546|      560|           576|   584|                                    625|             643|             661|                                                                              744|               767|                                                                                                                                                                                                 980|                      1013|                                                  1078|                                1117|                          
                                                                        49                                           97                                                                                                              211                                                                          296                                       342                        372                                           420                                                                                                                 538      551       562            578    586                                     627              645              663                                                                               749                784                                                                                                                                                                                                  987                       1024                                                   1081                                 1121                          


Chain C from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh...ee...........eeeeee............eeeeee.hhhhhhhhhhhh....eeeee......eeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee...eeeeeee..............hhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee......eeee.hhh........eeeee.....eeeeeee.....eeeeeeee........eeeeeeee.....eeeeeeee........eeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4tz4 C   48 NFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSEAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPD  428
                                    57        67        77        87        97       107       117       132       142       152       162       172|      185       195       205       221       231       241       251       261   ||  277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427 
                                                                                                        126|                                     172|                                  213|                                          265|                                                                                                                                                            
                                                                                                         132                                      176                                   220                                           272
   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 4TZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TZ4)

(-) Gene Ontology  (47, 53)

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
    LVY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln C:115 - Lys C:116   [ RasMol ]  
    Tyr A:660 - Ser A:661   [ 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
  4tz4
    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
  CRBN_HUMAN | Q96SW2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DDB1_HUMAN | Q16531
    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
  CRBN_HUMAN | Q96SW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DDB1_HUMAN | Q16531
    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
        CRBN_HUMAN | Q96SW2: 4m91 5fqd 5hxb 5v3o
        DDB1_HUMAN | Q16531: 2b5l 2b5m 2b5n 2hye 3e0c 3ei1 3ei2 3ei3 3ei4 3i7h 3i7k 3i7l 3i7n 3i7o 3i7p 3i89 3i8c 3i8e 4a08 4a09 4a0a 4a0b 4a0k 4a0l 4a11 4ci1 4ci2 4ci3 4e54 4e5z 5fqd 5hxb 5jk7 5v3o

(-) Related Entries Specified in the PDB File

4tzc 4tzu