1VYBA

Endonuclease domain of human line1 orf2p
Total Genus 73
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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
73
sequence length
236
structure length
236
Chain Sequence
GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR
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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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molecule tags Transferase
molecule keywords ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
publication title Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
pubmed doi rcsb
source organism Homo sapiens
total genus 73
structure length 236
sequence length 236
chains with identical sequence B
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2004-04-25

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 1vybA00
4QHDA 1E9NA 4GEWA 2DDTA 4LNDA 3I48A 2IMQX 2DDRA 2F2FB 3K55A 2J63A 4L21A 3G00A 2DDSA 4L1ZA 5INPA 4GZ0A 5EWTA 1ATND 3I5VA 5INKA 3N9VA 5DFIA 4K6LF 5INLA 1DE9A 4IEMA 1WDUA 5DFJA 3L1WA 4L1YA 4QH9A 4L20A 1DEWA 4GYZA 2XSWA 1DNKA 2V0SA 2F1NA 5A7IA 4QHEA 2UYRX 5CFGA 2VOAA 3NGQA 4F1HA 3G0AA 3WCXA 4GZ1A 5INOA 5DV4A 5DG0A 5J42A 4B5FA 3FZIA 3G2CA 4B5MA 3G3CA 1DE8A 3I41A 3G91A 5DFFA 4B5IA 5J3SA 5J3PA 1VYBA 2ISIA 3NGOA 3G1KA 2D1KB 4B5JA 4F1IA 2DNJA 3G2DA 4FPVA 5DFHA 2A3ZB 3G8VA 4AWNA 4GZ2A 4JG3A 3GA6A 3MTCA 3W2YA 3W3DB 5INMA 3U8UA 5INNA 3MPRA 3CJCD 4F1HB 3G6SA 5A7JA 1SR4B 2A40B 2O3HA 1AKOA 1I9YA 3G38A 3G4TA 1Y21A 1NTFA 3DNIA 4FVAA 4PUQA 1BIXA 2O3CA 3TEBA 4A9CA 4CMNA 4RUWA 3NGNA 2A41B 3W2XA 3G0RA 5CFEA 4C1RA 4CMLA 3I46A 3NR8A 4F1RA 5HT2A 2JC4A 1I9ZA 5J3ZA 3G3YA 1ZWXA 2EI9A 2V0RA 1SI6X 5DV2A 5INQA 2JC5A 1YJHA 4B5GA 1HD7A 5J8NA 2A42B 4B5HA
chains in the Genus database with same CATH superfamily
4QHDA 1E9NA 4GEWA 2DDTA 4LNDA 3I48A 2IMQX 2DDRA 2F2FB 3K55A 2J63A 4L21A 3G00A 2DDSA 4L1ZA 5INPA 4GZ0A 5EWTA 1ATND 3I5VA 5INKA 3N9VA 5DFIA 4K6LF 5INLA 1DE9A 4IEMA 1WDUA 5DFJA 3L1WA 4L1YA 4QH9A 4L20A 1DEWA 4GYZA 2XSWA 1DNKA 2V0SA 2F1NA 5A7IA 4QHEA 2UYRX 5CFGA 2VOAA 3NGQA 4F1HA 3G0AA 3WCXA 4GZ1A 5INOA 5DV4A 5DG0A 5J42A 4B5FA 3FZIA 3G2CA 4B5MA 3G3CA 1DE8A 3I41A 3G91A 5DFFA 4B5IA 5J3SA 5J3PA 1VYBA 2ISIA 3NGOA 3G1KA 2D1KB 4B5JA 4F1IA 2DNJA 3G2DA 4FPVA 5DFHA 2A3ZB 3G8VA 4AWNA 4GZ2A 4JG3A 3GA6A 3MTCA 3W2YA 3W3DB 5INMA 3U8UA 5INNA 3MPRA 3CJCD 4F1HB 3G6SA 5A7JA 1SR4B 2A40B 2O3HA 1AKOA 1I9YA 3G38A 3G4TA 1Y21A 1NTFA 3DNIA 4FVAA 4PUQA 1BIXA 2O3CA 3TEBA 4A9CA 4CMNA 4RUWA 3NGNA 2A41B 3W2XA 3G0RA 5CFEA 4C1RA 4CMLA 3I46A 3NR8A 4F1RA 5HT2A 2JC4A 1I9ZA 5J3ZA 3G3YA 1ZWXA 2EI9A 2V0RA 1SI6X 5DV2A 5INQA 2JC5A 1YJHA 4B5GA 1HD7A 5J8NA 2A42B 4B5HA
chains in the Genus database with same CATH topology
4QHDA 1E9NA 4GEWA 2DDTA 4LNDA 3I48A 2IMQX 2DDRA 2F2FB 3K55A 2J63A 4L21A 3G00A 2DDSA 4L1ZA 5INPA 4GZ0A 5EWTA 1ATND 3I5VA 5INKA 3N9VA 5DFIA 4K6LF 5INLA 1DE9A 4IEMA 1WDUA 5DFJA 3L1WA 4L1YA 4QH9A 4L20A 1DEWA 4GYZA 2XSWA 1DNKA 2V0SA 2F1NA 5A7IA 4QHEA 2UYRX 5CFGA 2VOAA 3NGQA 4F1HA 3G0AA 3WCXA 4GZ1A 5INOA 5DV4A 5DG0A 5J42A 4B5FA 3FZIA 3G2CA 4B5MA 3G3CA 1DE8A 3I41A 3G91A 5DFFA 4B5IA 5J3SA 5J3PA 1VYBA 2ISIA 3NGOA 3G1KA 2D1KB 4B5JA 4F1IA 2DNJA 3G2DA 4FPVA 5DFHA 2A3ZB 3G8VA 4AWNA 4GZ2A 4JG3A 3GA6A 3MTCA 3W2YA 3W3DB 5INMA 3U8UA 5INNA 3MPRA 3CJCD 4F1HB 3G6SA 5A7JA 1SR4B 2A40B 2O3HA 1AKOA 1I9YA 3G38A 3G4TA 1Y21A 1NTFA 3DNIA 4FVAA 4PUQA 1BIXA 2O3CA 3TEBA 4A9CA 4CMNA 4RUWA 3NGNA 2A41B 3W2XA 3G0RA 5CFEA 4C1RA 4CMLA 3I46A 3NR8A 4F1RA 5HT2A 2JC4A 1I9ZA 5J3ZA 3G3YA 1ZWXA 2EI9A 2V0RA 1SI6X 5DV2A 5INQA 2JC5A 1YJHA 4B5GA 1HD7A 5J8NA 2A42B 4B5HA
chains in the Genus database with same CATH homology


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