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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1)
 
Authors :  R. Molina, S. Stella, P. Redondo, H. Gomez, M. J. Marcaida, M. Orozco, J. G. Montoya
Date :  26 May 14  (Deposition) - 03 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Keywords :  Hydrolase-Dna Complex, Catalysis, Protein-Dna Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Molina, S. Stella, P. Redondo, H. Gomez, M. J. Marcaida, M. Orozco, J. Prieto, G. Montoya
Visualizing Phosphodiester-Bond Hydrolysis By An Endonuclease.
Nat. Struct. Mol. Biol. V. 22 65 2015
PubMed-ID: 25486305  |  Reference-DOI: 10.1038/NSMB.2932

(-) Compounds

Molecule 1 - HOMING ENDONUCLEASE I-DMOI
    ChainsA, D
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System VectorPET24D
    Expression System Vector TypePLASMID
    Organism ScientificDESULFUROCOCCUS MOBILIS
    Organism Taxid2274
 
Molecule 2 - 25MER
    ChainsB, E, H
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 25MER
    ChainsC, F, I
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - HOMING ENDONUCLEASE I-DMOI
    ChainsG
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System VectorPET24D
    Expression System Vector TypePLASMID
    Organism ScientificDESULFUROCOCCUS MOBILIS
    Organism Taxid2274

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit ABCDEFGHI
Biological Unit 1 (1x)ABC      
Biological Unit 2 (1x)   DEF   
Biological Unit 3 (1x)      GHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ALA A:116 , HOH A:2005 , DA B:14 , DC C:16BINDING SITE FOR RESIDUE ZN A1188
2AC2SOFTWAREASP D:21 , ALA D:116 , HOH D:2003 , HOH D:2018 , DA E:14 , DC F:16BINDING SITE FOR RESIDUE ZN D1197
3AC3SOFTWAREASP G:21 , GLN G:42 , ALA G:116 , HOH G:2005 , DA H:14 , DC I:16BINDING SITE FOR RESIDUE ZN G1182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UN7)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:31 -Asn A:32
2Lys D:30 -Gly D:31
3Gly D:31 -Asn D:32
4Lys G:30 -Gly G:31
5Gly G:31 -Asn G:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UN7)

(-) Exons   (0, 0)

(no "Exon" information available for 4UN7)

(-) 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:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh....eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4un7 A   4 NENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    

Chain B from PDB  Type:DNA  Length:25
                                                         
                 4un7 B   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     

Chain C from PDB  Type:DNA  Length:25
                                                         
                 4un7 C   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    10        20     

Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4un7 D   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPPEAAALEHH 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 

Chain E from PDB  Type:DNA  Length:25
                                                         
                 4un7 E   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     

Chain F from PDB  Type:DNA  Length:25
                                                         
                 4un7 F   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    10        20     

Chain G from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4un7 G   5 EEVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSH 181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       

Chain H from PDB  Type:DNA  Length:25
                                                         
                 4un7 H   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     

Chain I from PDB  Type:DNA  Length:25
                                                         
                 4un7 I   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    10        20     

   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 4UN7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UN7)

(-) Gene Ontology  (6, 6)

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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:31 - Asn A:32   [ RasMol ]  
    Gly D:31 - Asn D:32   [ RasMol ]  
    Gly G:31 - Asn G:32   [ RasMol ]  
    Lys D:30 - Gly D:31   [ RasMol ]  
    Lys G:30 - Gly G:31   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4un7
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DMO1_DESMO | P21505
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.-.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DMO1_DESMO | P21505
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DMO1_DESMO | P215051b24 1mow 2vs7 2vs8 4d6n 4d6o 4un8 4un9 4una 4unb 4unc 4ut0 5a0w 5ak9 5akf 5akm 5akn

(-) Related Entries Specified in the PDB File

4un6 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7)
4un8 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2)
4un9 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)
4una THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)
4unb THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 6 DAYS INCUBATION IN 5MM MN (STATE 5)
4unc THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6)