4B5MA

Neisseria ap endonuclease bound to the substrate with a cytosine orphan base
Total Genus 81

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

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
AH2 (20-27)S1 (2-8)TVIII1 (29-32)TIV10 (245-248)S2 (31-35)TIV1 (9-12)AH1 (12-18)3H2 (46-48)3H3 (51-53)TVIII2 (73-76)3H1 (41-43)TIV3 (63-66)S4 (69-73)TIV2 (48-51)EMPTYAH3 (87-91)S7 (103-109)S5 (79-82)S6 (95-100)AH4 (117-140)TII'1 (100-103)TI1 (113-116)TI5 (184-187)S8 (143-149)TII1 (168-171)3H4 (156-158)TIV5 (159-162)AH5 (173-184)AH6 (191-195)TI2 (162-165)TI4 (165-168)S10 (221-225)S9 (189-190)TI6 (196-199)TI8 (212-215)TIV8 (208-211)TIV9 (211-214)TVIII3 (240-243)AH7 (227-232)S11 (233-238)TIV7 (169-172)S12 (250-254)S3 (55-59)Updating...
connected with : NaN
molecule tags Hydrolase/dna
source organism Neisseria meningitidis
publication title Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
pubmed doi rcsb
molecule keywords PUTATIVE EXODEOXYRIBONUCLEASE
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
3W2XA 3G38A 4B5GA 3I48A 5A7JA 3I5VA 3G0AA 3G0RA 1DE9A 4FPVA 1ATND 4L1ZA 2JC4A 3I46A 4F1HB 4QHDA 3G2CA 5DFJA 3NR8A 2O3HA 1BIXA 4F1HA 5CFEA 4CMLA 5DFFA 3G6SA 4GZ0A 2A42B 3G8VA 4CMNA 4LNDA 5J42A 4L21A 1HD7A 2F2FB 4F1RA 3NGOA 1WDUA 3L1WA 2J63A 5J8NA 5J3ZA 5DV4A 3NGNA 2DDRA 3TEBA 2A3ZB 4QHEA 1DE8A 4A9CA 4B5FA 5INPA 3K55A 5INLA 4B5IA 2XSWA 3G1KA 3GA6A 4C1RA 2DDTA 3MPRA 5A7IA 2UYRX 5J3SA 4JG3A 4IEMA 4FVAA 4PUQA 1NTFA 3W3DB 5DV2A 2ISIA 3WCXA 5DG0A 4B5HA 3W2YA 4QH9A 2JC5A 3I41A 3DNIA 3NGQA 5J3PA 2DNJA 4GEWA 3CJCD 5INKA 3N9VA 4L1YA 5INMA 4B5MA 2A41B 1VYBA 2D1KB 2V0RA 1I9YA 5INNA 4GZ1A 1I9ZA 5DFIA 4L20A 2IMQX 3U8UA 1E9NA 3FZIA 3G2DA 3G00A 5INOA 1SI6X 2V0SA 1DEWA 4RUWA 1DNKA 3MTCA 4GYZA 4GZ2A 2A40B 2F1NA 1SR4B 4K6LF 2DDSA 1ZWXA 2EI9A 3G3CA 2VOAA 2O3CA 5INQA 4AWNA 1YJHA 3G4TA 1AKOA 3G3YA 3G91A 5EWTA 5DFHA 5HT2A 4F1IA 1Y21A 4B5JA 5CFGA
chains in the Genus database with same CATH superfamily
3W2XA 3G38A 4B5GA 3I48A 5A7JA 3I5VA 3G0AA 3G0RA 1DE9A 4FPVA 1ATND 4L1ZA 2JC4A 3I46A 4F1HB 4QHDA 3G2CA 5DFJA 3NR8A 2O3HA 1BIXA 4F1HA 5CFEA 4CMLA 5DFFA 3G6SA 4GZ0A 2A42B 3G8VA 4CMNA 4LNDA 5J42A 4L21A 1HD7A 2F2FB 4F1RA 3NGOA 1WDUA 3L1WA 2J63A 5J8NA 5J3ZA 5DV4A 3NGNA 2DDRA 3TEBA 2A3ZB 4QHEA 1DE8A 4A9CA 4B5FA 5INPA 3K55A 5INLA 4B5IA 2XSWA 3G1KA 3GA6A 4C1RA 2DDTA 3MPRA 5A7IA 2UYRX 5J3SA 4JG3A 4IEMA 4FVAA 4PUQA 1NTFA 3W3DB 5DV2A 2ISIA 3WCXA 5DG0A 4B5HA 3W2YA 4QH9A 2JC5A 3I41A 3DNIA 3NGQA 5J3PA 2DNJA 4GEWA 3CJCD 5INKA 3N9VA 4L1YA 5INMA 4B5MA 2A41B 1VYBA 2D1KB 2V0RA 1I9YA 5INNA 4GZ1A 1I9ZA 5DFIA 4L20A 2IMQX 3U8UA 1E9NA 3FZIA 3G2DA 3G00A 5INOA 1SI6X 2V0SA 1DEWA 4RUWA 1DNKA 3MTCA 4GYZA 4GZ2A 2A40B 2F1NA 1SR4B 4K6LF 2DDSA 1ZWXA 2EI9A 3G3CA 2VOAA 2O3CA 5INQA 4AWNA 1YJHA 3G4TA 1AKOA 3G3YA 3G91A 5EWTA 5DFHA 5HT2A 4F1IA 1Y21A 4B5JA 5CFGA
chains in the Genus database with same CATH topology
3W2XA 3G38A 4B5GA 3I48A 5A7JA 3I5VA 3G0AA 3G0RA 1DE9A 4FPVA 1ATND 4L1ZA 2JC4A 3I46A 4F1HB 4QHDA 3G2CA 5DFJA 3NR8A 2O3HA 1BIXA 4F1HA 5CFEA 4CMLA 5DFFA 3G6SA 4GZ0A 2A42B 3G8VA 4CMNA 4LNDA 5J42A 4L21A 1HD7A 2F2FB 4F1RA 3NGOA 1WDUA 3L1WA 2J63A 5J8NA 5J3ZA 5DV4A 3NGNA 2DDRA 3TEBA 2A3ZB 4QHEA 1DE8A 4A9CA 4B5FA 5INPA 3K55A 5INLA 4B5IA 2XSWA 3G1KA 3GA6A 4C1RA 2DDTA 3MPRA 5A7IA 2UYRX 5J3SA 4JG3A 4IEMA 4FVAA 4PUQA 1NTFA 3W3DB 5DV2A 2ISIA 3WCXA 5DG0A 4B5HA 3W2YA 4QH9A 2JC5A 3I41A 3DNIA 3NGQA 5J3PA 2DNJA 4GEWA 3CJCD 5INKA 3N9VA 4L1YA 5INMA 4B5MA 2A41B 1VYBA 2D1KB 2V0RA 1I9YA 5INNA 4GZ1A 1I9ZA 5DFIA 4L20A 2IMQX 3U8UA 1E9NA 3FZIA 3G2DA 3G00A 5INOA 1SI6X 2V0SA 1DEWA 4RUWA 1DNKA 3MTCA 4GYZA 4GZ2A 2A40B 2F1NA 1SR4B 4K6LF 2DDSA 1ZWXA 2EI9A 3G3CA 2VOAA 2O3CA 5INQA 4AWNA 1YJHA 3G4TA 1AKOA 3G3YA 3G91A 5EWTA 5DFHA 5HT2A 4F1IA 1Y21A 4B5JA 5CFGA
chains in the Genus database with same CATH homology


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