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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEIL1(P2G) BOUND TO DUPLEX DNA CONTAINING THF
 
Authors :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Ga
Date :  17 Mar 16  (Deposition) - 06 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Dna Glycosylase Neil1 Fpg Nei Base Excision Repair, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Q. Gao, C. Yi
Tautomerization-Dependent Recognition And Excision Of Oxidation Damage In Base-Excision Dna Repair
Proc. Natl. Acad. Sci. Usa V. 113 7792 2016
PubMed-ID: 27354518  |  Reference-DOI: 10.1073/PNAS.1604591113

(-) Compounds

Molecule 1 - ENDONUCLEASE 8-LIKE 1
    Chains: A, B, C
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NEIL1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA GLYCOSYLASE/AP LYASE NEIL1,DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE NEIL1,ENDONUCLEASE VIII-LIKE 1,FPG1,NEI HOMOLOG 1,NEH1, NEI-LIKE PROTEIN 1
 
Molecule 2 - DNA (26-MER)
    Chains: D, E
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5ITR)

(-) Sites  (0, 0)

(no "Site" information available for 5ITR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:95 -His A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITR)

(-) 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:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeeee...........eeeeeeeeeeee..eeeeeeee..........eeeeee......eeeee.......eeeeeee......eeeeee......eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhh........eeee.....eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5itr A   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPK 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     231       241       251       261       271       281       291
                                                                                                                                                                                                                                  202|                                                                    
                                                                                                                                                                                                                                   223                                                                    


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee........eeeeeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeee.......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhh.hhhhhh.........hhhhhhhhhhhh......hhhhhhh.....hhhhhhhhhhhhhhhh....................eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itr B   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQNPDLLELCHSVPKEVVQLGGRGYAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     230       240   ||  259       269       279       289 
                                                                                                                                                                                                                                  202|                   244|                                    
                                                                                                                                                                                                                                   222                    254                                    


Chain C from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..........................eeeeeee....eeeeeee........eeee.......eeee........eeeeee........eeeee........................hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh..................hhhhhhhhhhhhhhh..hhhhhhhh..........ee.....ee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itr C   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEKLQNPDLLELCHSVPKEVVQLDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQDPGPLAP 290
                                    11        21        31        41        51        61   ||   74        84        94       104       114       124       134       144       154       164       174       184       194    || 223       233     ||255       265       275      |286    
                                                                                          65|                                                                                                                               199|                 239|                           282|      
                                                                                           69                                                                                                                                219                  252                            284      


Chain D from PDB  Type:DNA  Length:26
                                                          
                 5itr D   1 CGTCCACGTCTACTAGACCTGGACGG  28
                                    10  ||    22      
                                       13|            
                                        16            


Chain E from PDB  Type:DNA  Length:26
                                                          
                 5itr E   1 CGTCCACGTCTACTAGACCTGGACGG  28
                                    10  ||    22      
                                       13|            
                                        16            


Chain F from PDB  Type:DNA  Length:26
                                                          
                 5itr F   1 CGTCCACGTCTACTAGACCTGGGCGG  28
                                    10  ||    22      
                                       13|            
                                        16
   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 5ITR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

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    Arg A:95 - His A:96   [ RasMol ]  
 
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  NEIL1_HUMAN | Q96FI4
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEIL1_HUMAN | Q96FI4: 1tdh 4nrv 5itq 5itt 5itu 5itx 5ity

(-) Related Entries Specified in the PDB File

5itq 5itt 5itu 5itx 5ity