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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CNOT6L IN COMPLEX WITH NEOMYCIN
 
Authors :  Q. Zhang, M. Bartlam
Date :  21 Sep 15  (Deposition) - 26 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Nuclease Domain, Deadenylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhang, D. Yan, E. Guo, B. Ding, W. Yang, R. Liu, T. Yamamoto, M. Bartla
Structural Basis For Inhibition Of The Deadenylase Activity Of Human Cnot6L
Febs Lett. V. 590 1270 2016
PubMed-ID: 27013054  |  Reference-DOI: 10.1002/1873-3468.12160

(-) Compounds

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE
    Chains: A
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CNOT6L, CCR4B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARBON CATABOLITE REPRESSOR PROTEIN 4 HOMOLOG B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NMY1Ligand/IonNEOMYCIN
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:206 , TYR A:207 , GLU A:240 , HIS A:360 , MET A:361 , TRP A:363 , PRO A:365 , LYS A:371 , ASP A:410 , ASN A:412 , LEU A:414 , ASN A:479 , PHE A:484 , ILE A:488 , SO4 A:602 , HOH A:724 , HOH A:742 , HOH A:754 , HOH A:816 , HOH A:844 , HOH A:901binding site for residue NMY A 601
2AC2SOFTWARETYR A:201 , TRP A:363 , NMY A:601binding site for residue SO4 A 602
3AC3SOFTWARETHR A:243 , GLU A:244 , LYS A:278 , HOH A:800 , HOH A:826 , HOH A:883binding site for residue SO4 A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DV4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:181 -Gln A:182
2Glu A:437 -Leu A:438
3Cys A:520 -Pro A:521

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DV4)

(-) Exons   (0, 0)

(no "Exon" information available for 5DV4)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......eeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhh.eeeeeee.......hhhhhhh.eeeeeeee...eeeeeeeeeehhhhhhhh...hhhhhhh......eeeeeeeee.hhhh.eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhheee..hhhhh....hhhhhhhh...eee....eee..........ee....ee..eeeeee...eeeeeee...hhhhhhhh................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dv4 A 169 LPPRPWITLKERDQSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKELRYNECLMNFSCEGRITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQLELHP 540
                                   178   ||  191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       352       362       372       382       392||     409       419       429       439       449|      466       476       486       496       506       516       526       536    
                                       182|                                                                                                                                                      339|                                       393|                                             449|                                                                                   
                                        186                                                                                                                                                       351                                        401                                              457
   Legend:   → Mismatch (orange background)
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  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 5DV4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DV4)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:181 - Gln A:182   [ RasMol ]  
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  5dv4
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  CNO6L_HUMAN | Q96LI5
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 Related Entries

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

UniProtKB/Swiss-Prot
        CNO6L_HUMAN | Q96LI5: 3ngn 3ngo 3ngq 5dv2

(-) Related Entries Specified in the PDB File

5dv2