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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEIL1 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 :  2.53
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 :  Neil1 Dna Glycosylase Base Excision Repair Fpg Nei, 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, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: E
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:9 , ALA A:10 , PHE A:13 , SER A:84 , PHE A:85 , GLY A:241 , ARG A:242 , HOH A:606 , HOH A:665binding site for residue GOL A 501
2AC2SOFTWARESER A:50 , ALA A:51 , GLN B:139binding site for residue GOL B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:67 -Pro A:68
2Arg A:95 -His A:96
3Gln C:67 -Pro C:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITT)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeeee............eeeeeeeeeee..eeeeeeee..........eeeeee.....eeeeee.......eeeeeee......eeeeee......eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhh........eeee.....eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itt A   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPK 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     230       240       250       260       270       280       290 
                                                                                                                                                                                                                                  202|                                                                     
                                                                                                                                                                                                                                   222                                                                     


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eee..ee............eeeeeeeeeee..eeeeeeee..........eeeeee.....eeeeee.......eeeeee.......eeeeee......eeee..............hhhhhhhhhhh...hhhhh.hhhhhh.........hhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhh...................eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itt 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee...........eeeeeeeeeeee..eeeeeeee.........eeeeee....eeeeeee.......eeeeeee......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhh.hhhhhh.........hhhhhhhhhhh.......hhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhh........eeee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itt C   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQKLQNPDLLELCHSVPKEVVQLDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQDPGPLAP 290
                                    11        21        31        41        51        61  ||    72        82        92       102       112       122       132       142       152       162       172       182       192       202|      228       238||     260       270       280 ||      
                                                                                         64|                                                                                                                                     202|                 239|                           282|      
                                                                                          66                                                                                                                                      219                  252                            284      


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


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


Chain F from PDB  Type:DNA  Length:26
                                                          
                 5itt F   1 CGTCCACGTCTACTAGACCTGGACGG  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 5ITT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5itq 5itr 5itu 5itx 5ity