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 :  NAB2 ZN FINGERS COMPLEXED WITH POLYADENOSINE
 
Authors :  M. Stewart, S. I. Kuhlmann, E. Valkov
Date :  04 Jul 13  (Deposition) - 09 Oct 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Zn Finger, Polyadenylation, Polyadenosine Rna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. I. Kuhlmann, E. Valkov, M. Stewart
Structural Basis For The Molecular Recognition Of Polyadenosine Rna By Nab2 Zn Fingers.
Nucleic Acids Res. V. 42 672 2014
PubMed-ID: 24071581  |  Reference-DOI: 10.1093/NAR/GKT876

(-) Compounds

Molecule 1 - NAB2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NAB2 ZN FINGERS 3-5, UNP RESIDUES 401-466
    Gene: CTHT_0057680, NAB2
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 2 - POLYADENOSINE RNA
    Chains: C, D, E
    Engineered: YES
    Other Details: AAAAAA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MG4Ligand/IonMAGNESIUM ION
3ZN6Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:405 , CYS A:411 , CYS A:416 , HIS A:420BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWARECYS A:426 , CYS A:432 , CYS A:437 , HIS A:441BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWARECYS A:446 , CYS A:451 , CYS A:456 , HIS A:460BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWARECYS A:405 , LYS A:406 , TRP A:408 , ACT A:505BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWARELEU A:442 , LYS A:443 , THR A:444 , ACT A:504BINDING SITE FOR RESIDUE ACT A 505
06AC6SOFTWARECYS B:405 , CYS B:411 , CYS B:416 , HIS B:420BINDING SITE FOR RESIDUE ZN B 501
07AC7SOFTWARECYS B:426 , CYS B:432 , CYS B:437 , HIS B:441 , HOH B:603BINDING SITE FOR RESIDUE ZN B 502
08AC8SOFTWARECYS B:446 , CYS B:451 , CYS B:456 , HIS B:460BINDING SITE FOR RESIDUE ZN B 503
09AC9SOFTWAREA C:3 , A C:4BINDING SITE FOR RESIDUE MG C 101
10BC1SOFTWAREA C:3 , A D:3BINDING SITE FOR RESIDUE MG C 102
11BC2SOFTWAREASN B:410 , A C:2BINDING SITE FOR RESIDUE MG C 103
12BC3SOFTWAREGLU A:462 , A D:3 , A D:4 , HOH D:203BINDING SITE FOR RESIDUE MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LJ0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:408 -Pro A:409
2Arg A:449 -Pro A:450
3Trp B:408 -Pro B:409
4Arg B:449 -Pro B:450

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4LJ0)

(-) 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:65
                                                                                                 
               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
                 4lj0 A 402 EQDCKYWPNCANPLCAFRHPTMPPCRNGGECKVPGCKFTHLKTPCKFRPCTNRSCPFLHEEGQRG 466
                                   411       421       431       441       451       461     


Chain B from PDB  Type:PROTEIN  Length:64
                                                                                                
               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
                 4lj0 B 402 EQDCKYWPNCANPLCAFRHPTMPPCRNGGECKVPGCKFTHLKTPCKFRPCTNRSCPFLHEEGQR 465
                                   411       421       431       441       451       461    


Chain C from PDB  Type:RNA  Length:4
                                    
                 4lj0 C   1 AAAA   4


Chain D from PDB  Type:RNA  Length:4
                                    
                 4lj0 D   1 AAAA   4


Chain E from PDB  Type:RNA  Length:2
                                  
                 4lj0 E   1 AA   2
   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 4LJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LJ0)

(-) Gene Ontology  (1, 1)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:449 - Pro A:450   [ RasMol ]  
    Arg B:449 - Pro B:450   [ RasMol ]  
    Trp A:408 - Pro A:409   [ RasMol ]  
    Trp B:408 - Pro B:409   [ 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
  4lj0
    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
  G0SCL7_CHATD | G0SCL7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  G0SCL7_CHATD | G0SCL7
    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 4LJ0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LJ0)