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(-) Description

Title :  HUMAN APE1 PRODUCT COMPLEX
 
Authors :  B. D. Freudenthal, S. H. Wilson
Date :  26 Aug 15  (Deposition) - 14 Oct 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B,D,P,V
Biol. Unit 1:  A,D,P,V  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Lyase/Dna, Lyase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Freudenthal, W. A. Beard, M. J. Cuneo, N. S. Dyrkheeva, S. H. Wilso
Capturing Snapshots Of Ape1 Processing Dna Damage.
Nat. Struct. Mol. Biol. V. 22 924 2015
PubMed-ID: 26458045  |  Reference-DOI: 10.1038/NSMB.3105

(-) Compounds

Molecule 1 - DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
    Chains: A, B
    EC Number: 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21-DE3
    Expression System Taxid: 469008
    Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE 1,APE- 1,REF-1,REDOX FACTOR-1
 
Molecule 2 - DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3')
    Chains: V
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABDPV
Biological Unit 1 (1x): A DPV
Biological Unit 2 (1x):  B   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4MG1Ligand/IonMAGNESIUM ION
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
13DR-1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:96 , HOH A:504 , HOH A:527 , HOH A:550 , 3DR D:1 , DC P:10binding site for residue MG A 401
2AC2SOFTWAREASP A:189 , PHE A:192 , ARG A:193 , LEU A:211 , GLY A:239 , PHE A:240 , LEU A:243 , HOH A:557binding site for residue PEG A 402
3AC3SOFTWAREGLU A:101 , TRP A:119 , HOH A:584 , HIS B:116 , ARG B:136binding site for residue CL A 403
4AC4SOFTWARELYS A:63 , GLU A:86 , GLU A:87 , LEU A:179 , HOH A:529 , HOH A:533binding site for residue EDO A 404
5AC5SOFTWARELEU A:44 , TYR A:45 , ASN A:277 , HOH A:518 , HOH A:524 , HOH A:636 , HOH A:665binding site for residue EDO A 405
6AC6SOFTWARETYR A:144 , GLU A:149 , HOH A:554 , HOH A:656 , HIS B:116 , GLN B:117 , TYR B:118binding site for residue PEG B 401
7AC7SOFTWARETHR B:97 , CYS B:99 , GLU B:101 , TRP B:119 , SER B:120 , ALA B:121 , VAL B:131binding site for residue EDO B 402
8AC8SOFTWARETRP B:188 , ASP B:189 , PHE B:240 , HOH B:504 , HOH B:556binding site for residue EDO B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:247 -Pro A:248
2Val B:247 -Pro B:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DFF)

(-) 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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhheeeee..........eeeee.....eeee............eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh...........hhhhhhhhh.....eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dff A  43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312      


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhheeeee......eeeee.....eeee.......eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh...........hhhhh.........eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dff B  43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSYSGVGLLSRQCPLKVSYGIGDEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122||     136       146 ||    161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       
                                                                                                          123|                 148|                                                                                                                                                                    
                                                                                                           128                  154                                                                                                                                                                    


Chain D from PDB  Type:DNA  Length:11
                                           
                 5dff D   1 xCGACGGATCC  11
                            |       10 
                            1-3DR      


Chain P from PDB  Type:DNA  Length:10
                                          
                 5dff P   1 GCTGATGCGC  10
                                    10


Chain V from PDB  Type:DNA  Length:21
                                                     
                 5dff V   1 GGATCCGTCGGGCGCATCAGC  21
                                    10        20
   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 5DFF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Asymmetric Unit(hide GO term definitions)

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    Val A:247 - Pro A:248   [ RasMol ]  
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  5dff
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  APEX1_HUMAN | P27695
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        APEX1_HUMAN | P27695: 1bix 1cqg 1cqh 1de8 1de9 1dew 1e9n 1hd7 2isi 2o3h 3u8u 4iem 4lnd 4qh9 4qhd 4qhe 5cfg 5dfh 5dfi 5dfj 5dg0

(-) Related Entries Specified in the PDB File

5dfh 5dfi 5dfj