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(-) Description

Title :  HUMAN APE1 PHOSPHOROTHIOATE SUBSTRATE 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 :  1.63
Chains :  Asym. Unit :  A,B,P,V
Biol. Unit 1:  A,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: 3.1.-.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 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(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z) P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 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

  1234
Asymmetric Unit : ABPV
Biological Unit 1 (1x): A PV
Biological Unit 2 (1x):  B  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
148Z1Mod. Nucleotide2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONO-ALPHA-D-ARABINOFURANOSE
2CL2Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
148Z1Mod. Nucleotide2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONO-ALPHA-D-ARABINOFURANOSE
2CL-1Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
148Z-1Mod. Nucleotide2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONO-ALPHA-D-ARABINOFURANOSE
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4OMC-1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:44 , TYR A:45 , ASN A:277 , HOH A:548 , HOH A:553 , HOH A:622 , HOH A:624binding site for residue EDO A 401
2AC2SOFTWAREASP A:189 , PHE A:192 , GLY A:239 , PHE A:240 , HOH A:507 , HOH A:546binding site for residue EDO A 402
3AC3SOFTWAREPHE A:266 , THR A:268 , TYR A:269 , ASP A:308 , DC P:12 , DG V:12binding site for residue EDO A 403
4AC4SOFTWAREGLU A:101 , TYR A:118 , TRP A:119 , HOH A:545 , HIS B:116 , ARG B:136binding site for residue CL A 404
5AC5SOFTWARETYR B:45 , ARG B:274 , ASN B:277 , HOH B:507 , HOH B:586binding site for residue EDO B 401
6AC6SOFTWAREASP B:189 , PHE B:192 , GLY B:239 , PHE B:240 , HOH B:571 , HOH B:623binding site for residue EDO B 402
7AC7SOFTWAREGLY B:145 , ARG B:156 , VAL B:157binding site for residue CL B 403
8AC8SOFTWAREARG B:177 , MET B:270 , MET B:271 , DG V:1 , DG V:2binding site for residue EDO V 101
9AC9SOFTWAREGLU A:96 , TYR A:171 , ASN A:174 , ARG A:177 , ARG A:181 , ASN A:212 , ALA A:230 , PHE A:266 , TRP A:280 , HIS A:309 , DG P:9 , DC P:12 , HOH P:101 , HOH P:109 , HOH P:111 , HOH P:112 , HOH P:113 , HOH P:116 , HOH P:120 , DG V:12binding site for residues OMC P 10 and 48Z P 11

(-) SS Bonds  (0, 0)

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

(-) 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 5DFI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DFI)

(-) 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....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh............hhhhhhhhhhhhhhh..eehhhhhh...........hhhhhhhhh.....eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dfi 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:265
                                                                                                                                                                                                                                                                                                         
               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
                 5dfi B  43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSGVGLLSRQCPLKVSYGIGDEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122|      138       148|      163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
                                                                                                         122|                148|                                                                                                                                                                    
                                                                                                          129                 154                                                                                                                                                                    


Chain P from PDB  Type:DNA/RNA  Length:21
                                                     
                 5dfi P   1 GCTGATGCGcxCGACGGATCC  21
                                    10|       20 
                                    10-OMC       
                                     11-48Z      


Chain V from PDB  Type:DNA  Length:21
                                                     
                 5dfi 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 5DFI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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        APEX1_HUMAN | P27695: 1bix 1cqg 1cqh 1de8 1de9 1dew 1e9n 1hd7 2isi 2o3h 3u8u 4iem 4lnd 4qh9 4qhd 4qhe 5cfg 5dff 5dfh 5dfj 5dg0

(-) Related Entries Specified in the PDB File

5dff 5dfh 5dfj