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(-) Description

Title :  FLAP ENDONUCLEASE 1 (FEN1) D233N WITH CLEAVED PRODUCT FRAGMENT AND SM3+
 
Authors :  S. E. Tsutakawa, A. S. Arvai, J. A. Tainer
Date :  31 May 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,D,E,F,G
Keywords :  Metalloprotein, Replication, Dna Damage, Dna Repair, Base Excision Repair, Protein-Dna, 5' Nuclease, Fen, Product, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Tsutakawa, A. S. Arvai, M. J. Thompson, L. D. Finger, F. Rashid, A. Neil, J. C. Kim, A. S. Sarker, S. M. Mirkin, S. M. Hamdan, J. A. Grasby, J. A. Tainer
Flap Endonuclease 1 D233N With Cleaved Product Fragment
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FLAP ENDONUCLEASE 1
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FEN1, RAD2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FEN-1,DNASE IV,FLAP STRUCTURE-SPECIFIC ENDONUCLEASE 1, MATURATION FACTOR 1,HFEN-1
 
Molecule 2 - DNA (5'- D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 5 - DNA (5'-D(P*TP*T)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ADEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2K1Ligand/IonPOTASSIUM ION
3SM8Ligand/IonSAMARIUM (III) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:2 , GLU A:160 , ASP A:181 , SM A:403 , SM A:404 , HOH A:689 , DT E:7binding site for residue SM A 401
02AC2SOFTWAREASP A:86 , GLU A:158 , GLU A:160 , SM A:404 , HOH A:525 , HOH E:113binding site for residue SM A 402
03AC3SOFTWAREGLU A:160 , ASP A:179 , ASP A:181 , SM A:401 , DT E:7binding site for residue SM A 403
04AC4SOFTWAREGLU A:158 , GLU A:160 , SM A:401 , SM A:402 , HOH A:525 , DT E:7 , HOH E:103 , HOH E:113binding site for residue SM A 404
05AC5SOFTWARESER A:237 , ILE A:238 , ILE A:241 , HOH A:640 , DT D:5 , HOH D:131binding site for residue K A 405
06AC6SOFTWAREGLU A:57 , GLU A:285 , GLU A:313 , GLN A:342 , HOH A:537 , HOH A:588 , HOH A:598binding site for residue SM A 406
07AC7SOFTWAREGLU A:57 , GLU A:59 , GLU A:313 , GLN A:342 , HOH A:589 , HOH A:639 , HOH A:668binding site for residue SM A 407
08AC8SOFTWAREGLY A:49 , ASP A:51 , HOH A:724 , HOH A:803binding site for residue SM A 408
09AC9SOFTWAREGLU A:102 , HOH A:545 , HOH A:891 , HOH A:901binding site for residue SM A 409
10AD1SOFTWAREGLY A:2 , ILE A:3 , ASP A:179 , MET A:180 , HOH A:596 , DG E:8binding site for residue EDO A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K97)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K97)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K97)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K97)

(-) Exons   (0, 0)

(no "Exon" information available for 5K97)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...eee.hhhhhh..eeeeehhhhhhhhhhhhee..ee........hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh...eeee............eeeehhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh................hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k97 A   2 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSNYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ 342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5k97 D   1 ACTCTGCCTCAAGACGGT  18
                                    10        


Chain E from PDB  Type:DNA  Length:11
                                           
                 5k97 E   7 TGAGGCAGAGT  17
                                    16 


Chain F from PDB  Type:DNA  Length:7
                                       
                 5k97 F   1 ACCGTCC   7


Chain G from PDB  Type:DNA  Length:2
                                  
                 5k97 G   5 TT   6
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  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 5K97)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K97)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K97)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FEN1_HUMAN | P39748: 1u7b 1ul1 3q8k 3q8l 3q8m 3uvu 5e0v 5fv7 5kse 5um9

(-) Related Entries Specified in the PDB File

5k96