Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RCL WITH 6-CYCLOPENTYL-AMP
 
Authors :  G. Labesse, A. Padilla, P. A. Kaminski
Date :  04 Jul 12  (Deposition) - 02 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Deoxyribonucleoside 5'-Monophosphate N-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Padilla, C. Amiable, S. Pochet, P. A. Kaminski, G. Labesse
Structure Of The Oncoprotein Rcl Bound To Three Nucleotide Analogues.
Acta Crystallogr. , Sect. D V. 69 247 2013
PubMed-ID: 23385460  |  Reference-DOI: 10.1107/S0907444912045039

(-) Compounds

Molecule 1 - DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 11-151
    Gene: RCL
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: C-MYC-RESPONSIVE PROTEIN RCL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
16C64Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
16C62Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
16C62Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , GLY A:16 , SER A:17 , ILE A:18 , ARG A:19 , GLY A:20 , ILE A:65 , ASN A:69 , SER A:87 , GLY A:89 , GLU A:93 , HOH A:309 , HOH A:310 , HOH A:327 , HOH A:373 , HOH A:375 , SER B:117 , MET B:119BINDING SITE FOR RESIDUE 6C6 A 201
2AC2SOFTWARESER A:117 , MET A:119 , CYS B:15 , GLY B:16 , SER B:17 , ILE B:18 , ARG B:19 , GLY B:20 , VAL B:46 , ILE B:65 , ASN B:69 , SER B:87 , GLY B:89 , GLU B:93 , HOH B:304 , HOH B:308 , HOH B:364 , HOH B:410BINDING SITE FOR RESIDUE 6C6 B 201
3AC3SOFTWARECYS C:15 , GLY C:16 , SER C:17 , ILE C:18 , ARG C:19 , GLY C:20 , ILE C:65 , ASN C:69 , SER C:87 , GLY C:89 , GLU C:93 , HOH C:303 , HOH C:344 , HOH C:377 , HOH C:391 , HOH C:407 , SER D:117 , MET D:119BINDING SITE FOR RESIDUE 6C6 C 201
4AC4SOFTWARESER C:117 , MET C:119 , HOH C:423 , TYR D:13 , CYS D:15 , GLY D:16 , SER D:17 , ILE D:18 , ARG D:19 , GLY D:20 , ILE D:65 , ASN D:69 , SER D:87 , GLY D:89 , GLU D:93 , HOH D:337 , HOH D:345 , HOH D:362 , HOH D:373BINDING SITE FOR RESIDUE 6C6 D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FYI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:149 -Tyr A:150
2Gly D:126 -Ser D:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYI)

(-) Sequences/Alignments

Asymmetric 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:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyi A  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    19        29        39   ||   65        75        85        95       105       115       125       135       145     
                                                            43|                                                                                          
                                                             60                                                                                          


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee.hhhhhh.hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyi B  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    19        29        39        60        70        80        90       100       110       120       130       140       150
                                                                 48|                                                                                          
                                                                  60                                                                                          


Chain C from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyi C  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEA 149
                                    19        29        39    ||  65        75        85        95       105       115       125       135       145    
                                                             44|                                                                                        
                                                              61                                                                                        


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fyi D  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEA 149
                                    19        29        39     || 63        73        83        93       103       113       123       133       143      
                                                              45|                                                                                         
                                                               60
   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 4FYI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    6C6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:149 - Tyr A:150   [ RasMol ]  
    Gly D:126 - Ser D:127   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4fyi
    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
  DNPH1_RAT | O35820
    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)
  3.2.2.-
    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
  DNPH1_RAT | O35820
    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
        DNPH1_RAT | O35820: 2khz 2klh 4fyh 4fyk 4kxl 4kxm 4kxn 4p5d

(-) Related Entries Specified in the PDB File

2klh 4fyh 4fyk