5DFH | Genus

Total Genus 84

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	84
sequence length	276
structure length	275
Chain Sequence	ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLARKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

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

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

Genus data interpretation

Chord Diagram

molecule tags	Lyase/dna
source organism	Homo sapiens
publication title	Capturing snapshots of APE1 processing DNA damage. pubmed doi rcsb
molecule keywords	DNA-(apurinic or apyrimidinic site) lyase
total genus	84
structure length	275
sequence length	276
chains with identical sequence	B
ec nomenclature	ec 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
pdb deposition date	2015-08-26

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	Class	Architecture	Topology	Homology	Domain
3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I; Chain A	Endonuclease/exonuclease/phosphatase	5dfhA00

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

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

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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5DFHA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations