1E9NA

A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, ape1, and its implications for the catalytic mechanism
Total Genus 85
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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
85
sequence length
276
structure length
274
Chain Sequence
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
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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 Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
pubmed doi rcsb
molecule tags Dna repair
source organism Homo sapiens
molecule keywords DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
total genus 85
structure length 274
sequence length 276
chains with identical sequence B
ec nomenclature ec 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
pdb deposition date 2000-10-24

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 1e9nA00
4PUQA 3W3DB 4K6LF 2V0RA 3MTCA 1SI6X 2DNJA 2A3ZB 1Y21A 4L1ZA 5HT2A 4FPVA 4LNDA 3TEBA 2A42B 2J63A 5INPA 2ISIA 2V0SA 5INNA 4F1IA 4B5GA 3W2XA 2IMQX 4GZ1A 5DG0A 4L1YA 4L20A 1DE9A 2A40B 2F1NA 5J3ZA 5INKA 5DFHA 3FZIA 3G3CA 3L1WA 4QHDA 2UYRX 5DV4A 4B5MA 5DFIA 5J3PA 4CMNA 2XSWA 1DEWA 2JC5A 3WCXA 3G2CA 5A7JA 5INLA 5J42A 3W2YA 3DNIA 3I46A 1DNKA 5A7IA 3G8VA 1HD7A 4IEMA 5CFEA 5INQA 3I5VA 5DV2A 1BIXA 3K55A 3G3YA 3G2DA 4B5FA 3CJCD 3U8UA 4F1HA 5INMA 4AWNA 4RUWA 4B5JA 4JG3A 4QHEA 4GZ2A 3G1KA 1ZWXA 3G4TA 4FVAA 4CMLA 4A9CA 5J8NA 3G91A 3NGOA 4QH9A 1ATND 4F1HB 1I9ZA 1YJHA 2JC4A 2A41B 2VOAA 5J3SA 3MPRA 2DDSA 3G38A 5EWTA 2DDRA 2D1KB 5CFGA 4C1RA 2EI9A 3GA6A 4F1RA 1I9YA 4GYZA 2O3CA 3NR8A 1NTFA 4GEWA 3G6SA 4L21A 3G0AA 2DDTA 1SR4B 1VYBA 3NGNA 1DE8A 5INOA 1WDUA 2O3HA 5DFFA 5DFJA 1AKOA 3I41A 3NGQA 4GZ0A 3I48A 4B5HA 1E9NA 3G00A 3G0RA 4B5IA 2F2FB 3N9VA
chains in the Genus database with same CATH superfamily
4PUQA 3W3DB 4K6LF 2V0RA 3MTCA 1SI6X 2DNJA 2A3ZB 1Y21A 4L1ZA 5HT2A 4FPVA 4LNDA 3TEBA 2A42B 2J63A 5INPA 2ISIA 2V0SA 5INNA 4F1IA 4B5GA 3W2XA 2IMQX 4GZ1A 5DG0A 4L1YA 4L20A 1DE9A 2A40B 2F1NA 5J3ZA 5INKA 5DFHA 3FZIA 3G3CA 3L1WA 4QHDA 2UYRX 5DV4A 4B5MA 5DFIA 5J3PA 4CMNA 2XSWA 1DEWA 2JC5A 3WCXA 3G2CA 5A7JA 5INLA 5J42A 3W2YA 3DNIA 3I46A 1DNKA 5A7IA 3G8VA 1HD7A 4IEMA 5CFEA 5INQA 3I5VA 5DV2A 1BIXA 3K55A 3G3YA 3G2DA 4B5FA 3CJCD 3U8UA 4F1HA 5INMA 4AWNA 4RUWA 4B5JA 4JG3A 4QHEA 4GZ2A 3G1KA 1ZWXA 3G4TA 4FVAA 4CMLA 4A9CA 5J8NA 3G91A 3NGOA 4QH9A 1ATND 4F1HB 1I9ZA 1YJHA 2JC4A 2A41B 2VOAA 5J3SA 3MPRA 2DDSA 3G38A 5EWTA 2DDRA 2D1KB 5CFGA 4C1RA 2EI9A 3GA6A 4F1RA 1I9YA 4GYZA 2O3CA 3NR8A 1NTFA 4GEWA 3G6SA 4L21A 3G0AA 2DDTA 1SR4B 1VYBA 3NGNA 1DE8A 5INOA 1WDUA 2O3HA 5DFFA 5DFJA 1AKOA 3I41A 3NGQA 4GZ0A 3I48A 4B5HA 1E9NA 3G00A 3G0RA 4B5IA 2F2FB 3N9VA
chains in the Genus database with same CATH topology
4PUQA 3W3DB 4K6LF 2V0RA 3MTCA 1SI6X 2DNJA 2A3ZB 1Y21A 4L1ZA 5HT2A 4FPVA 4LNDA 3TEBA 2A42B 2J63A 5INPA 2ISIA 2V0SA 5INNA 4F1IA 4B5GA 3W2XA 2IMQX 4GZ1A 5DG0A 4L1YA 4L20A 1DE9A 2A40B 2F1NA 5J3ZA 5INKA 5DFHA 3FZIA 3G3CA 3L1WA 4QHDA 2UYRX 5DV4A 4B5MA 5DFIA 5J3PA 4CMNA 2XSWA 1DEWA 2JC5A 3WCXA 3G2CA 5A7JA 5INLA 5J42A 3W2YA 3DNIA 3I46A 1DNKA 5A7IA 3G8VA 1HD7A 4IEMA 5CFEA 5INQA 3I5VA 5DV2A 1BIXA 3K55A 3G3YA 3G2DA 4B5FA 3CJCD 3U8UA 4F1HA 5INMA 4AWNA 4RUWA 4B5JA 4JG3A 4QHEA 4GZ2A 3G1KA 1ZWXA 3G4TA 4FVAA 4CMLA 4A9CA 5J8NA 3G91A 3NGOA 4QH9A 1ATND 4F1HB 1I9ZA 1YJHA 2JC4A 2A41B 2VOAA 5J3SA 3MPRA 2DDSA 3G38A 5EWTA 2DDRA 2D1KB 5CFGA 4C1RA 2EI9A 3GA6A 4F1RA 1I9YA 4GYZA 2O3CA 3NR8A 1NTFA 4GEWA 3G6SA 4L21A 3G0AA 2DDTA 1SR4B 1VYBA 3NGNA 1DE8A 5INOA 1WDUA 2O3HA 5DFFA 5DFJA 1AKOA 3I41A 3NGQA 4GZ0A 3I48A 4B5HA 1E9NA 3G00A 3G0RA 4B5IA 2F2FB 3N9VA
chains in the Genus database with same CATH homology


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