4B5JA

Neisseria ap endonuclease bound to the substrate with an orphan adenine base
Total Genus 86
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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
86
sequence length
256
structure length
256
Chain Sequence
MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDY
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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 Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
pubmed doi rcsb
molecule tags Hydrolase/dna
source organism Neisseria meningitidis
molecule keywords PUTATIVE EXODEOXYRIBONUCLEASE
total genus 86
structure length 256
sequence length 256
ec nomenclature ec 3.1.11.2: Exodeoxyribonuclease III.
pdb deposition date 2012-08-03

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 4b5jA00
4F1HA 5J3ZA 5A7IA 3G00A 1NTFA 2XSWA 2EI9A 3G6SA 5J3SA 1DEWA 3G3YA 4PUQA 5INQA 1HD7A 1Y21A 1DE9A 3DNIA 2DNJA 5DFFA 1SI6X 3MTCA 3G2CA 2JC5A 4GEWA 5EWTA 2A3ZB 2DDRA 4B5FA 3W3DB 2V0SA 1I9YA 2F1NA 2D1KB 5INNA 3FZIA 5A7JA 1WDUA 4K6LF 3G3CA 1DE8A 4F1HB 1ZWXA 2O3CA 2DDSA 4B5MA 4F1RA 2V0RA 5DFJA 3NR8A 5CFEA 4AWNA 3TEBA 3G0AA 4L1ZA 4L20A 4L21A 3U8UA 3NGQA 3G91A 1DNKA 3MPRA 2UYRX 4B5JA 1AKOA 4F1IA 4CMNA 3N9VA 3I5VA 3G38A 4FVAA 2IMQX 4CMLA 2VOAA 1I9ZA 3G0RA 2A40B 5INKA 2F2FB 4GZ1A 4B5IA 4L1YA 1YJHA 5DV2A 5CFGA 2JC4A 5HT2A 3WCXA 3G1KA 5INLA 3I48A 4QH9A 5DV4A 4QHEA 4IEMA 1BIXA 5DG0A 3W2XA 3G2DA 3GA6A 1ATND 5INOA 4GZ2A 2DDTA 3W2YA 4B5HA 5J8NA 3NGOA 4FPVA 5INMA 5DFHA 3I41A 5INPA 2J63A 3L1WA 1E9NA 1SR4B 4GZ0A 4GYZA 3CJCD 4RUWA 4C1RA 4B5GA 2O3HA 2A42B 5J42A 2A41B 3NGNA 5J3PA 3I46A 4A9CA 3K55A 2ISIA 3G8VA 4JG3A 3G4TA 5DFIA 4QHDA 4LNDA 1VYBA
chains in the Genus database with same CATH superfamily
4F1HA 5J3ZA 5A7IA 3G00A 1NTFA 2XSWA 2EI9A 3G6SA 5J3SA 1DEWA 3G3YA 4PUQA 5INQA 1HD7A 1Y21A 1DE9A 3DNIA 2DNJA 5DFFA 1SI6X 3MTCA 3G2CA 2JC5A 4GEWA 5EWTA 2A3ZB 2DDRA 4B5FA 3W3DB 2V0SA 1I9YA 2F1NA 2D1KB 5INNA 3FZIA 5A7JA 1WDUA 4K6LF 3G3CA 1DE8A 4F1HB 1ZWXA 2O3CA 2DDSA 4B5MA 4F1RA 2V0RA 5DFJA 3NR8A 5CFEA 4AWNA 3TEBA 3G0AA 4L1ZA 4L20A 4L21A 3U8UA 3NGQA 3G91A 1DNKA 3MPRA 2UYRX 4B5JA 1AKOA 4F1IA 4CMNA 3N9VA 3I5VA 3G38A 4FVAA 2IMQX 4CMLA 2VOAA 1I9ZA 3G0RA 2A40B 5INKA 2F2FB 4GZ1A 4B5IA 4L1YA 1YJHA 5DV2A 5CFGA 2JC4A 5HT2A 3WCXA 3G1KA 5INLA 3I48A 4QH9A 5DV4A 4QHEA 4IEMA 1BIXA 5DG0A 3W2XA 3G2DA 3GA6A 1ATND 5INOA 4GZ2A 2DDTA 3W2YA 4B5HA 5J8NA 3NGOA 4FPVA 5INMA 5DFHA 3I41A 5INPA 2J63A 3L1WA 1E9NA 1SR4B 4GZ0A 4GYZA 3CJCD 4RUWA 4C1RA 4B5GA 2O3HA 2A42B 5J42A 2A41B 3NGNA 5J3PA 3I46A 4A9CA 3K55A 2ISIA 3G8VA 4JG3A 3G4TA 5DFIA 4QHDA 4LNDA 1VYBA
chains in the Genus database with same CATH topology
4F1HA 5J3ZA 5A7IA 3G00A 1NTFA 2XSWA 2EI9A 3G6SA 5J3SA 1DEWA 3G3YA 4PUQA 5INQA 1HD7A 1Y21A 1DE9A 3DNIA 2DNJA 5DFFA 1SI6X 3MTCA 3G2CA 2JC5A 4GEWA 5EWTA 2A3ZB 2DDRA 4B5FA 3W3DB 2V0SA 1I9YA 2F1NA 2D1KB 5INNA 3FZIA 5A7JA 1WDUA 4K6LF 3G3CA 1DE8A 4F1HB 1ZWXA 2O3CA 2DDSA 4B5MA 4F1RA 2V0RA 5DFJA 3NR8A 5CFEA 4AWNA 3TEBA 3G0AA 4L1ZA 4L20A 4L21A 3U8UA 3NGQA 3G91A 1DNKA 3MPRA 2UYRX 4B5JA 1AKOA 4F1IA 4CMNA 3N9VA 3I5VA 3G38A 4FVAA 2IMQX 4CMLA 2VOAA 1I9ZA 3G0RA 2A40B 5INKA 2F2FB 4GZ1A 4B5IA 4L1YA 1YJHA 5DV2A 5CFGA 2JC4A 5HT2A 3WCXA 3G1KA 5INLA 3I48A 4QH9A 5DV4A 4QHEA 4IEMA 1BIXA 5DG0A 3W2XA 3G2DA 3GA6A 1ATND 5INOA 4GZ2A 2DDTA 3W2YA 4B5HA 5J8NA 3NGOA 4FPVA 5INMA 5DFHA 3I41A 5INPA 2J63A 3L1WA 1E9NA 1SR4B 4GZ0A 4GYZA 3CJCD 4RUWA 4C1RA 4B5GA 2O3HA 2A42B 5J42A 2A41B 3NGNA 5J3PA 3I46A 4A9CA 3K55A 2ISIA 3G8VA 4JG3A 3G4TA 5DFIA 4QHDA 4LNDA 1VYBA
chains in the Genus database with same CATH homology


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