1DEWA

Crystal structure of human ape1 bound to abasic dna
Total Genus 82
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
82
sequence length
278
structure length
278
Chain Sequence
GPALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
pubmed doi rcsb
molecule tags Lyase/dna
source organism Homo sapiens
molecule keywords 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3'
total genus 82
structure length 278
sequence length 278
chains with identical sequence B
ec nomenclature ec 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
pdb deposition date 1999-11-15

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.10.10 Alpha Beta 4-Layer Sandwich Deoxyribonuclease I; Chain A Endonuclease/exonuclease/phosphatase 1dewA00
3G3YA 3NGNA 4F1IA 4IEMA 3G00A 4GZ1A 3G1KA 5DV4A 2EI9A 4C1RA 4QHDA 4L21A 4JG3A 3GA6A 3W3DB 3MTCA 4FVAA 3U8UA 4GEWA 3I5VA 4B5HA 2JC4A 3G0AA 1VYBA 3DNIA 2J63A 4PUQA 5J3SA 5INQA 2UYRX 4RUWA 3WCXA 5INLA 5EWTA 3NGOA 5A7JA 1E9NA 5J8NA 2A40B 3L1WA 2F2FB 4QH9A 4CMNA 2F1NA 1DEWA 3G6SA 2DNJA 3G0RA 4F1RA 1ZWXA 3FZIA 1WDUA 3G38A 3CJCD 2O3CA 5INMA 3G2DA 1NTFA 4QHEA 4GZ0A 3I41A 2A41B 4GYZA 3N9VA 1ATND 2XSWA 3G2CA 2VOAA 1AKOA 1I9YA 2DDSA 2O3HA 3G3CA 1Y21A 5CFGA 4F1HA 1I9ZA 4A9CA 4B5IA 1SR4B 4CMLA 5J42A 4FPVA 1BIXA 5J3PA 4B5FA 2JC5A 5INOA 4B5GA 2D1KB 1DNKA 5INPA 5CFEA 3W2YA 2V0RA 3I46A 2V0SA 3I48A 3K55A 3MPRA 5DFFA 3TEBA 5DFHA 3G8VA 2A3ZB 3NR8A 1DE9A 1DE8A 3W2XA 5DFJA 4B5JA 4F1HB 5DFIA 5DV2A 5INNA 4GZ2A 3NGQA 2A42B 2DDRA 1YJHA 2ISIA 2IMQX 4L1ZA 5A7IA 3G91A 4L20A 4LNDA 5J3ZA 4AWNA 5DG0A 5INKA 1HD7A 5HT2A 3G4TA 1SI6X 4K6LF 2DDTA 4B5MA 4L1YA
chains in the Genus database with same CATH superfamily
3G3YA 3NGNA 4F1IA 4IEMA 3G00A 4GZ1A 3G1KA 5DV4A 2EI9A 4C1RA 4QHDA 4L21A 4JG3A 3GA6A 3W3DB 3MTCA 4FVAA 3U8UA 4GEWA 3I5VA 4B5HA 2JC4A 3G0AA 1VYBA 3DNIA 2J63A 4PUQA 5J3SA 5INQA 2UYRX 4RUWA 3WCXA 5INLA 5EWTA 3NGOA 5A7JA 1E9NA 5J8NA 2A40B 3L1WA 2F2FB 4QH9A 4CMNA 2F1NA 1DEWA 3G6SA 2DNJA 3G0RA 4F1RA 1ZWXA 3FZIA 1WDUA 3G38A 3CJCD 2O3CA 5INMA 3G2DA 1NTFA 4QHEA 4GZ0A 3I41A 2A41B 4GYZA 3N9VA 1ATND 2XSWA 3G2CA 2VOAA 1AKOA 1I9YA 2DDSA 2O3HA 3G3CA 1Y21A 5CFGA 4F1HA 1I9ZA 4A9CA 4B5IA 1SR4B 4CMLA 5J42A 4FPVA 1BIXA 5J3PA 4B5FA 2JC5A 5INOA 4B5GA 2D1KB 1DNKA 5INPA 5CFEA 3W2YA 2V0RA 3I46A 2V0SA 3I48A 3K55A 3MPRA 5DFFA 3TEBA 5DFHA 3G8VA 2A3ZB 3NR8A 1DE9A 1DE8A 3W2XA 5DFJA 4B5JA 4F1HB 5DFIA 5DV2A 5INNA 4GZ2A 3NGQA 2A42B 2DDRA 1YJHA 2ISIA 2IMQX 4L1ZA 5A7IA 3G91A 4L20A 4LNDA 5J3ZA 4AWNA 5DG0A 5INKA 1HD7A 5HT2A 3G4TA 1SI6X 4K6LF 2DDTA 4B5MA 4L1YA
chains in the Genus database with same CATH topology
3G3YA 3NGNA 4F1IA 4IEMA 3G00A 4GZ1A 3G1KA 5DV4A 2EI9A 4C1RA 4QHDA 4L21A 4JG3A 3GA6A 3W3DB 3MTCA 4FVAA 3U8UA 4GEWA 3I5VA 4B5HA 2JC4A 3G0AA 1VYBA 3DNIA 2J63A 4PUQA 5J3SA 5INQA 2UYRX 4RUWA 3WCXA 5INLA 5EWTA 3NGOA 5A7JA 1E9NA 5J8NA 2A40B 3L1WA 2F2FB 4QH9A 4CMNA 2F1NA 1DEWA 3G6SA 2DNJA 3G0RA 4F1RA 1ZWXA 3FZIA 1WDUA 3G38A 3CJCD 2O3CA 5INMA 3G2DA 1NTFA 4QHEA 4GZ0A 3I41A 2A41B 4GYZA 3N9VA 1ATND 2XSWA 3G2CA 2VOAA 1AKOA 1I9YA 2DDSA 2O3HA 3G3CA 1Y21A 5CFGA 4F1HA 1I9ZA 4A9CA 4B5IA 1SR4B 4CMLA 5J42A 4FPVA 1BIXA 5J3PA 4B5FA 2JC5A 5INOA 4B5GA 2D1KB 1DNKA 5INPA 5CFEA 3W2YA 2V0RA 3I46A 2V0SA 3I48A 3K55A 3MPRA 5DFFA 3TEBA 5DFHA 3G8VA 2A3ZB 3NR8A 1DE9A 1DE8A 3W2XA 5DFJA 4B5JA 4F1HB 5DFIA 5DV2A 5INNA 4GZ2A 3NGQA 2A42B 2DDRA 1YJHA 2ISIA 2IMQX 4L1ZA 5A7IA 3G91A 4L20A 4LNDA 5J3ZA 4AWNA 5DG0A 5INKA 1HD7A 5HT2A 3G4TA 1SI6X 4K6LF 2DDTA 4B5MA 4L1YA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3G3Y A;  3NGN A;  4F1I A;  4IEM A;  3G00 A;  4GZ1 A;  3G1K A;  5DV4 A;  2EI9 A;  4C1R A;  4QHD A;  4L21 A;  4JG3 A;  3GA6 A;  3W3D B;  3MTC A;  4FVA A;  3U8U A;  4GEW A;  3I5V A;  4B5H A;  2JC4 A;  3G0A A;  1VYB A;  3DNI A;  2J63 A;  4PUQ A;  5J3S A;  5INQ A;  2UYR X;  4RUW A;  3WCX A;  5INL A;  5EWT A;  3NGO A;  5A7J A;  1E9N A;  5J8N A;  2A40 B;  3L1W A;  2F2F B;  4QH9 A;  4CMN A;  2F1N A;  1DEW A;  3G6S A;  2DNJ A;  3G0R A;  4F1R A;  1ZWX A;  3FZI A;  1WDU A;  3G38 A;  3CJC D;  2O3C A;  5INM A;  3G2D A;  1NTF A;  4QHE A;  4GZ0 A;  3I41 A;  2A41 B;  4GYZ A;  3N9V A;  1ATN D;  2XSW A;  3G2C A;  2VOA A;  1AKO A;  1I9Y A;  2DDS A;  2O3H A;  3G3C A;  1Y21 A;  5CFG A;  4F1H A;  1I9Z A;  4A9C A;  4B5I A;  1SR4 B;  4CML A;  5J42 A;  4FPV A;  1BIX A;  5J3P A;  4B5F A;  2JC5 A;  5INO A;  4B5G A;  2D1K B;  1DNK A;  5INP A;  5CFE A;  3W2Y A;  2V0R A;  3I46 A;  2V0S A;  3I48 A;  3K55 A;  3MPR A;  5DFF A;  3TEB A;  5DFH A;  3G8V A;  2A3Z B;  3NR8 A;  1DE9 A;  1DE8 A;  3W2X A;  5DFJ A;  4B5J A;  4F1H B;  5DFI A;  5DV2 A;  5INN A;  4GZ2 A;  3NGQ A;  2A42 B;  2DDR A;  1YJH A;  2ISI A;  2IMQ X;  4L1Z A;  5A7I A;  3G91 A;  4L20 A;  4LND A;  5J3Z A;  4AWN A;  5DG0 A;  5INK A;  1HD7 A;  5HT2 A;  3G4T A;  1SI6 X;  4K6L F;  2DDT A;  4B5M A;  4L1Y A; 
#chains in the Genus database with same CATH topology
 3G3Y A;  3NGN A;  4F1I A;  4IEM A;  3G00 A;  4GZ1 A;  3G1K A;  5DV4 A;  2EI9 A;  4C1R A;  4QHD A;  4L21 A;  4JG3 A;  3GA6 A;  3W3D B;  3MTC A;  4FVA A;  3U8U A;  4GEW A;  3I5V A;  4B5H A;  2JC4 A;  3G0A A;  1VYB A;  3DNI A;  2J63 A;  4PUQ A;  5J3S A;  5INQ A;  2UYR X;  4RUW A;  3WCX A;  5INL A;  5EWT A;  3NGO A;  5A7J A;  1E9N A;  5J8N A;  2A40 B;  3L1W A;  2F2F B;  4QH9 A;  4CMN A;  2F1N A;  1DEW A;  3G6S A;  2DNJ A;  3G0R A;  4F1R A;  1ZWX A;  3FZI A;  1WDU A;  3G38 A;  3CJC D;  2O3C A;  5INM A;  3G2D A;  1NTF A;  4QHE A;  4GZ0 A;  3I41 A;  2A41 B;  4GYZ A;  3N9V A;  1ATN D;  2XSW A;  3G2C A;  2VOA A;  1AKO A;  1I9Y A;  2DDS A;  2O3H A;  3G3C A;  1Y21 A;  5CFG A;  4F1H A;  1I9Z A;  4A9C A;  4B5I A;  1SR4 B;  4CML A;  5J42 A;  4FPV A;  1BIX A;  5J3P A;  4B5F A;  2JC5 A;  5INO A;  4B5G A;  2D1K B;  1DNK A;  5INP A;  5CFE A;  3W2Y A;  2V0R A;  3I46 A;  2V0S A;  3I48 A;  3K55 A;  3MPR A;  5DFF A;  3TEB A;  5DFH A;  3G8V A;  2A3Z B;  3NR8 A;  1DE9 A;  1DE8 A;  3W2X A;  5DFJ A;  4B5J A;  4F1H B;  5DFI A;  5DV2 A;  5INN A;  4GZ2 A;  3NGQ A;  2A42 B;  2DDR A;  1YJH A;  2ISI A;  2IMQ X;  4L1Z A;  5A7I A;  3G91 A;  4L20 A;  4LND A;  5J3Z A;  4AWN A;  5DG0 A;  5INK A;  1HD7 A;  5HT2 A;  3G4T A;  1SI6 X;  4K6L F;  2DDT A;  4B5M A;  4L1Y A; 
#chains in the Genus database with same CATH homology
 3G3Y A;  3NGN A;  4F1I A;  4IEM A;  3G00 A;  4GZ1 A;  3G1K A;  5DV4 A;  2EI9 A;  4C1R A;  4QHD A;  4L21 A;  4JG3 A;  3GA6 A;  3W3D B;  3MTC A;  4FVA A;  3U8U A;  4GEW A;  3I5V A;  4B5H A;  2JC4 A;  3G0A A;  1VYB A;  3DNI A;  2J63 A;  4PUQ A;  5J3S A;  5INQ A;  2UYR X;  4RUW A;  3WCX A;  5INL A;  5EWT A;  3NGO A;  5A7J A;  1E9N A;  5J8N A;  2A40 B;  3L1W A;  2F2F B;  4QH9 A;  4CMN A;  2F1N A;  1DEW A;  3G6S A;  2DNJ A;  3G0R A;  4F1R A;  1ZWX A;  3FZI A;  1WDU A;  3G38 A;  3CJC D;  2O3C A;  5INM A;  3G2D A;  1NTF A;  4QHE A;  4GZ0 A;  3I41 A;  2A41 B;  4GYZ A;  3N9V A;  1ATN D;  2XSW A;  3G2C A;  2VOA A;  1AKO A;  1I9Y A;  2DDS A;  2O3H A;  3G3C A;  1Y21 A;  5CFG A;  4F1H A;  1I9Z A;  4A9C A;  4B5I A;  1SR4 B;  4CML A;  5J42 A;  4FPV A;  1BIX A;  5J3P A;  4B5F A;  2JC5 A;  5INO A;  4B5G A;  2D1K B;  1DNK A;  5INP A;  5CFE A;  3W2Y A;  2V0R A;  3I46 A;  2V0S A;  3I48 A;  3K55 A;  3MPR A;  5DFF A;  3TEB A;  5DFH A;  3G8V A;  2A3Z B;  3NR8 A;  1DE9 A;  1DE8 A;  3W2X A;  5DFJ A;  4B5J A;  4F1H B;  5DFI A;  5DV2 A;  5INN A;  4GZ2 A;  3NGQ A;  2A42 B;  2DDR A;  1YJH A;  2ISI A;  2IMQ X;  4L1Z A;  5A7I A;  3G91 A;  4L20 A;  4LND A;  5J3Z A;  4AWN A;  5DG0 A;  5INK A;  1HD7 A;  5HT2 A;  3G4T A;  1SI6 X;  4K6L F;  2DDT A;  4B5M A;  4L1Y A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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