4B5MA

Neisseria ap endonuclease bound to the substrate with a cytosine orphan base
Total Genus 81
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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
81
sequence length
257
structure length
257
Chain Sequence
MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDYA
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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 Hydrolase/dna
molecule keywords PUTATIVE EXODEOXYRIBONUCLEASE
publication title Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
pubmed doi rcsb
source organism Neisseria meningitidis
total genus 81
structure length 257
sequence length 257
chains with identical sequence B, C
ec nomenclature
pdb deposition date 2012-08-06

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 4b5mA00
3G3CA 5DFFA 4B5HA 1YJHA 2JC4A 5INMA 4GZ0A 2O3HA 4QH9A 3G2DA 2A40B 2O3CA 4CMNA 5J8NA 1SI6X 3G91A 1SR4B 3L1WA 4PUQA 3G00A 3W3DB 3DNIA 3MPRA 5CFGA 3G2CA 3WCXA 3NGOA 5INNA 2XSWA 2D1KB 1AKOA 4L21A 4B5GA 2F2FB 1Y21A 4CMLA 1VYBA 4AWNA 1WDUA 5DFHA 4QHDA 5A7IA 3I5VA 2A41B 5J3SA 5DFJA 5INOA 4F1IA 4RUWA 1HD7A 5INPA 3W2YA 4F1HA 4GZ1A 2A42B 5A7JA 4B5JA 4FPVA 4L1YA 3G4TA 4B5IA 3G0RA 3K55A 4FVAA 5J3PA 5CFEA 2A3ZB 3NR8A 3G0AA 3G8VA 2J63A 3CJCD 4GYZA 3NGQA 1DEWA 3FZIA 5INLA 4B5FA 2JC5A 3MTCA 5INKA 4LNDA 1E9NA 4QHEA 3NGNA 1I9YA 1I9ZA 5DG0A 2V0SA 2F1NA 2DDTA 5HT2A 4L20A 4F1RA 5J42A 5DFIA 3N9VA 4GZ2A 3TEBA 1ZWXA 3GA6A 2DDSA 4JG3A 4B5MA 1DE8A 2IMQX 4GEWA 4C1RA 4F1HB 1ATND 5DV4A 5DV2A 3G6SA 4L1ZA 4A9CA 3G38A 5J3ZA 2V0RA 4IEMA 2DNJA 3G1KA 2DDRA 1DE9A 3I46A 1DNKA 1BIXA 3G3YA 1NTFA 5EWTA 2EI9A 3W2XA 2UYRX 4K6LF 5INQA 2VOAA 2ISIA 3U8UA 3I48A 3I41A
chains in the Genus database with same CATH superfamily
3G3CA 5DFFA 4B5HA 1YJHA 2JC4A 5INMA 4GZ0A 2O3HA 4QH9A 3G2DA 2A40B 2O3CA 4CMNA 5J8NA 1SI6X 3G91A 1SR4B 3L1WA 4PUQA 3G00A 3W3DB 3DNIA 3MPRA 5CFGA 3G2CA 3WCXA 3NGOA 5INNA 2XSWA 2D1KB 1AKOA 4L21A 4B5GA 2F2FB 1Y21A 4CMLA 1VYBA 4AWNA 1WDUA 5DFHA 4QHDA 5A7IA 3I5VA 2A41B 5J3SA 5DFJA 5INOA 4F1IA 4RUWA 1HD7A 5INPA 3W2YA 4F1HA 4GZ1A 2A42B 5A7JA 4B5JA 4FPVA 4L1YA 3G4TA 4B5IA 3G0RA 3K55A 4FVAA 5J3PA 5CFEA 2A3ZB 3NR8A 3G0AA 3G8VA 2J63A 3CJCD 4GYZA 3NGQA 1DEWA 3FZIA 5INLA 4B5FA 2JC5A 3MTCA 5INKA 4LNDA 1E9NA 4QHEA 3NGNA 1I9YA 1I9ZA 5DG0A 2V0SA 2F1NA 2DDTA 5HT2A 4L20A 4F1RA 5J42A 5DFIA 3N9VA 4GZ2A 3TEBA 1ZWXA 3GA6A 2DDSA 4JG3A 4B5MA 1DE8A 2IMQX 4GEWA 4C1RA 4F1HB 1ATND 5DV4A 5DV2A 3G6SA 4L1ZA 4A9CA 3G38A 5J3ZA 2V0RA 4IEMA 2DNJA 3G1KA 2DDRA 1DE9A 3I46A 1DNKA 1BIXA 3G3YA 1NTFA 5EWTA 2EI9A 3W2XA 2UYRX 4K6LF 5INQA 2VOAA 2ISIA 3U8UA 3I48A 3I41A
chains in the Genus database with same CATH topology
3G3CA 5DFFA 4B5HA 1YJHA 2JC4A 5INMA 4GZ0A 2O3HA 4QH9A 3G2DA 2A40B 2O3CA 4CMNA 5J8NA 1SI6X 3G91A 1SR4B 3L1WA 4PUQA 3G00A 3W3DB 3DNIA 3MPRA 5CFGA 3G2CA 3WCXA 3NGOA 5INNA 2XSWA 2D1KB 1AKOA 4L21A 4B5GA 2F2FB 1Y21A 4CMLA 1VYBA 4AWNA 1WDUA 5DFHA 4QHDA 5A7IA 3I5VA 2A41B 5J3SA 5DFJA 5INOA 4F1IA 4RUWA 1HD7A 5INPA 3W2YA 4F1HA 4GZ1A 2A42B 5A7JA 4B5JA 4FPVA 4L1YA 3G4TA 4B5IA 3G0RA 3K55A 4FVAA 5J3PA 5CFEA 2A3ZB 3NR8A 3G0AA 3G8VA 2J63A 3CJCD 4GYZA 3NGQA 1DEWA 3FZIA 5INLA 4B5FA 2JC5A 3MTCA 5INKA 4LNDA 1E9NA 4QHEA 3NGNA 1I9YA 1I9ZA 5DG0A 2V0SA 2F1NA 2DDTA 5HT2A 4L20A 4F1RA 5J42A 5DFIA 3N9VA 4GZ2A 3TEBA 1ZWXA 3GA6A 2DDSA 4JG3A 4B5MA 1DE8A 2IMQX 4GEWA 4C1RA 4F1HB 1ATND 5DV4A 5DV2A 3G6SA 4L1ZA 4A9CA 3G38A 5J3ZA 2V0RA 4IEMA 2DNJA 3G1KA 2DDRA 1DE9A 3I46A 1DNKA 1BIXA 3G3YA 1NTFA 5EWTA 2EI9A 3W2XA 2UYRX 4K6LF 5INQA 2VOAA 2ISIA 3U8UA 3I48A 3I41A
chains in the Genus database with same CATH homology


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

 
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