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 :  STRUCTURE OF THE HOIP PUB DOMAIN BOUND TO SPATA2 PIM PEPTIDE
 
Authors :  P. R. Elliott, D. Komander
Date :  18 Jul 16  (Deposition) - 24 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Pub Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Elliott, D. Leske, M. Hrdinka, K. Bagola, B. K. Fiil, S. H. Mclaughlin, J. Wagstaff, N. Volkmar, J. C. Christianson, B. M. Kessler, S. M. Freund, D. Komander, M. Gyrd-Hansen
Spata2 Links Cyld To Lubac, Activates Cyld, And Controls Lubac Signaling.
Mol. Cell V. 63 990 2016
PubMed-ID: 27591049  |  Reference-DOI: 10.1016/J.MOLCEL.2016.08.001

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RNF31
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA II
    Gene: RNF31, ZIBRA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HOIL-1-INTERACTING PROTEIN,HOIP,RING FINGER PROTEIN 31,ZINC IN-BETWEEN-RING-FINGER UBIQUITIN-ASSOCIATED DOMAIN PROTEIN
 
Molecule 2 - SPERMATOGENESIS-ASSOCIATED PROTEIN 2
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 334-341
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPERMATOGENESIS-ASSOCIATED PROTEIN PD1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:91 , TRP A:95binding site for residue SO4 A 201
2AC2SOFTWAREARG B:91 , TRP B:95binding site for residue SO4 B 201
3AC3SOFTWAREARG B:116 , ARG B:120binding site for residue SO4 B 202
4AC4SOFTWARELYS A:81 , VAL C:335 , ASP D:334 , VAL D:335binding site for residue GOL C 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:59 -B:59

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LJN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LJN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LJN)

(-) Exons   (0, 0)

(no "Exon" information available for 5LJN)

(-) 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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........eee..hhhhhhh.....hhhhhhhhhh..ee...eee........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljn A   4 GEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQ 176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   


Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........eee..hhhhhhhh....hhhhhhhhhh..ee...eee........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljn B   4 GEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLL 164
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163 


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 5ljn C 334 DVDLYTDS 341


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5ljn D 334 DVDLYTD 340
   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 5LJN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LJN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LJN)

(-) Gene Ontology  (27, 29)

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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ljn)
 
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
  5ljn
    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
  RNF31_HUMAN | Q96EP0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SPAT2_HUMAN | Q9UM82
    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)
  6.3.2.-
    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
  RNF31_HUMAN | Q96EP0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SPAT2_HUMAN | Q9UM82
    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
        RNF31_HUMAN | Q96EP0: 2ct7 4dbg 4juy 4ljo 4ljp 4ljq 4owf 4oyj 4oyk 4p09 4p0a 4p0b 5edv
        SPAT2_HUMAN | Q9UM82: 5ljm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LJN)