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 :  CRYSTAL STRUCTURE OF GEMIN5 WD40 REPEATS IN COMPLEX WITH M7GPPPG
 
Authors :  X. Chao, W. Tempel, C. Bian, H. He, T. Cerovina, A. Seitova, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)
Date :  21 Sep 16  (Deposition) - 19 Oct 16  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Xu, H. Ishikawa, K. Izumikawa, L. Li, H. He, Y. Nobe, Y. Yamauchi, H. M. Shahjee, X. H. Wu, Y. T. Yu, T. Isobe, N. Takahashi, J. Min
Structural Insights Into Gemin5-Guided Selection Of Pre-Snrnas For Snrnp Assembly.
Genes Dev. V. 30 2376 2016
PubMed-ID: 27881600  |  Reference-DOI: 10.1101/GAD.288340.116

(-) Compounds

Molecule 1 - GEM-ASSOCIATED PROTEIN 5
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFBOH-LIC
    Expression System Taxid: 7108
    Gene: GEMIN5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric/Biological Unit (3, 23)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2GTG1Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
3UNX19Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:474 , THR A:540 , GLU A:541 , ASN A:582 , LYS A:641 , THR A:643 , TYR A:660 , ARG A:684 , HOH A:996 , HOH A:1003binding site for residue GTG A 801
2AC2SOFTWAREPRO A:12 , ASN A:13 , TRP A:14 , ARG A:359 , HOH A:935binding site for residue GOL A 802
3AC3SOFTWARETYR A:15 , SER A:113 , PHE A:155 , HOH A:967 , HOH A:976 , HOH A:978binding site for residue GOL A 803
4AC4SOFTWARESER A:293 , ASN A:294 , PRO A:342 , GLN A:350binding site for residue GOL A 804

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:240 -A:256

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:25 -Gly A:26
2Pro A:483 -Pro A:484
3Ile A:565 -Pro A:566

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TEF)

(-) 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:680
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...........eeee...eeeeee..eeeeeee.hhhh.......eeeeeee......eeeeee........eeeeee....eeeee....eeeeee......eeeeee......eeeeee...eeeeee....eeeeee.....eeeeee......eeeeee....eeeee......eeeee......eeeeee.......eeeeee...eeeeee.....eeeeee......................ee.......eeeee.hhh.eeeee.....eeee.............eeeeeeee.....eeeeeee...eeeeee....eeeeeee.....eeeeee......eeeeee....eeeee.........eeee.......eeeeee......eeeeee....eeeee.......ee........eeeeeee.........eeeeee....eeee........eeehhhhhhhhhh.......eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......hhhhh.eeeeee....eeeeehhhhhhhh....eee....eee......eeeeee......eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.hhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tef A   3 QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPGECYLATGSKDQTIRIWSCSRGRGVMILKLPFLKRRGGGIDPTVKERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQRRKYTLFSASSEGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHQGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQ 722
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |242       252       262       272       282       292       302       312  ||   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484 ||    502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722
                                                                                                                                                                                                                                        209|                                                                        315|                                                                                                                                                                     486|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                         240                                                                         318                                                                                                                                                                      495
   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 5TEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ 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
    Gly A:25 - Gly A:26   [ RasMol ]  
    Ile A:565 - Pro A:566   [ RasMol ]  
    Pro A:483 - Pro A:484   [ 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
  5tef
    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
  GEMI5_HUMAN | Q8TEQ6
    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)
  (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
  GEMI5_HUMAN | Q8TEQ6
    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
        GEMI5_HUMAN | Q8TEQ6: 5gxh 5gxi 5h1j 5h1k 5h1l 5h1m 5h3s 5h3t 5h3u 5tee 5tha

(-) Related Entries Specified in the PDB File

5tee