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 THE RING FINGER DOMAIN OF SLX1 IN COMPLEX WITH THE C-TERMINAL DOMAIN OF SLX4
 
Authors :  F. M. Lian, S. Xie, C. M. Qian
Date :  19 Apr 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ring Finger, Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. M. Lian, S. Xie, C. M. Qian
Crystal Structure And Sumo Binding Of Slx1-Slx4 Complex
Sci Rep V. 6 19331 2016
PubMed-ID: 26787556  |  Reference-DOI: 10.1038/SREP19331

(-) Compounds

Molecule 1 - STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1
    Chains: A, C
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 176-247
    Gene: SLX1, SPAP27G11.15
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
 
Molecule 2 - STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX4
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 356-419
    Gene: SLX4, SPAC688.06C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: SYNTHETIC LETHAL OF UNKNOWN FUNCTION PROTEIN 4

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:180 , CYS A:183 , HIS A:206 , CYS A:209binding site for residue ZN A 301
02AC2SOFTWARECYS A:196 , CYS A:201 , CYS A:228 , CYS A:231binding site for residue ZN A 302
03AC3SOFTWAREVAL B:372 , LYS B:375 , ASP B:383 , TRP B:390binding site for residue GOL B 501
04AC4SOFTWARETHR A:199 , ALA B:367 , LYS B:368 , ASP B:369 , LYS B:394binding site for residue GOL B 502
05AC5SOFTWAREGLN B:388 , SER B:399 , LEU B:400 , HOH B:601 , PHE C:245binding site for residue GOL B 503
06AC6SOFTWARECYS C:180 , CYS C:183 , HIS C:206 , CYS C:209binding site for residue ZN C 301
07AC7SOFTWARECYS C:196 , CYS C:201 , CYS C:228 , CYS C:231binding site for residue ZN C 302
08AC8SOFTWARELYS D:375 , ILE D:382 , ASP D:383 , TRP D:390binding site for residue GOL D 501
09AC9SOFTWAREPHE A:245 , GLN D:388 , SER D:399 , LEU D:400 , HOH D:623binding site for residue GOL D 502
10AD1SOFTWAREALA D:367 , LYS D:368 , ASP D:369 , LYS D:394binding site for residue SO4 D 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZDT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDT)

(-) 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:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee........eehhhhhhhhhh.........eee......eee.hhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4zdt A 178 VKCNLCYECIESDELRANCPFTDCNSINHLTCLASSFLTEECQVLPIEGMCTKCKRVLRWREFLSTVFT 246
                                   187       197       207       217       227       237         


Chain B from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4zdt B 349 GSMIVTQTHRAISQVVKQAKDNSVWIKILTYSAIDVEEFQLWLKRKNLNVSLDLIKSWCDKYGVLMKGS 417
                                   358       368       378       388       398       408         


Chain C from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee........eehhhhhhhhhh.........eee......eee.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4zdt C 177 PVKCNLCYECIESDELRANCPFTDCNSINHLTCLASSFLTEECQVLPIEGMCTKCKRVLRWREFLSTVFT 246
                                   186       196       206       216       226       236       246


Chain D from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4zdt D 349 GSMIVTQTHRAISQVVKQAKDNSVWIKILTYSAIDVEEFQLWLKRKNLNVSLDLIKSWCDKYGVLMKGS 417
                                   358       368       378       388       398       408
   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 4ZDT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 35)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4zdt)
 
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
  4zdt
    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
  SLX1_SCHPO | Q9P7M3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SLX4_SCHPO | Q9P6M0
    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)
  3.1.-.-
    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
  SLX1_SCHPO | Q9P7M3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SLX4_SCHPO | Q9P6M0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4ZDT)

(-) Related Entries Specified in the PDB File

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