4B5GA

Substrate bound neisseria ap endonuclease in absence of metal ions (crystal form 2)
Total Genus 82

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
82
sequence length
259
structure length
259
Chain Sequence
MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDYAAE

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)S12 (221-225)TIV1 (9-12)EMPTYTVIII6 (245-248)S2 (31-35)AH1 (12-17)3H2 (46-48)3H3 (51-53)TVIII2 (73-76)3H1 (41-43)TIV3 (61-64)S3 (55-59)S4 (69-73)TIV2 (48-51)S6 (95-100)AH3 (87-91)TIV4 (63-66)S7 (103-109)TII'1 (100-103)TVIII3 (77-80)AH4 (117-139)TIV5 (113-116)TII1 (168-171)O1 (254-256)S8 (143-149)TI1 (155-158)AH6 (191-195)TI9 (212-215)TVIII4 (159-162)S11 (217-218)TI4 (162-165)TI5 (163-166)TI6 (165-168)AH5 (173-186)S9 (189-190)S13 (233-238)TI7 (196-199)S10 (204-205)TII'2 (208-211)TI8 (211-214)TIV7 (210-213)AH7 (227-231)TVIII5 (240-243)S5 (79-82)TIV6 (169-172)S14 (250-254)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 EXODEOXYRIBONUCLEASE
total genus 82
structure length 259
sequence length 259
chains with identical sequence B, C
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 4b5gA00
1AKOA 5INKA 5J3PA 5DFHA 4IEMA 4GZ2A 4GZ1A 3MPRA 3W3DB 2A3ZB 4AWNA 2JC5A 3I41A 3NGQA 3I46A 5A7IA 3N9VA 3MTCA 4QHEA 3G91A 4CMNA 5HT2A 1DE9A 3W2YA 1WDUA 4FVAA 5CFGA 5EWTA 1NTFA 3G2DA 4A9CA 4B5IA 3G0AA 3K55A 3U8UA 3DNIA 5DV2A 3G38A 1HD7A 2ISIA 4F1IA 4QH9A 3WCXA 4L21A 2A42B 5DG0A 1DEWA 2DDSA 2EI9A 2UYRX 3I5VA 4FPVA 3G8VA 4B5FA 2D1KB 4B5HA 2F1NA 3L1WA 1DE8A 3G1KA 3G6SA 4JG3A 4L1YA 3TEBA 2A40B 3NGOA 2J63A 5DFJA 5DFIA 3I48A 3NGNA 4GZ0A 1VYBA 2V0RA 1BIXA 3G4TA 2V0SA 1DNKA 3G00A 1ZWXA 5J3SA 5J3ZA 4B5MA 1I9ZA 5A7JA 5INOA 2IMQX 2DNJA 3GA6A 1SR4B 5J8NA 2XSWA 1Y21A 3NR8A 5INMA 3G3YA 5INLA 4GEWA 3G3CA 1SI6X 4C1RA 5INQA 1ATND 2A41B 4PUQA 5J42A 4B5JA 2O3CA 4QHDA 5CFEA 5DFFA 5DV4A 4B5GA 4RUWA 4F1HA 2DDTA 4L1ZA 1E9NA 1I9YA 3W2XA 2VOAA 4F1RA 2F2FB 4CMLA 2JC4A 3CJCD 3FZIA 4LNDA 5INPA 2DDRA 1YJHA 4F1HB 3G0RA 4K6LF 4GYZA 4L20A 5INNA 2O3HA 3G2CA
chains in the Genus database with same CATH superfamily
1AKOA 5INKA 5J3PA 5DFHA 4IEMA 4GZ2A 4GZ1A 3MPRA 3W3DB 2A3ZB 4AWNA 2JC5A 3I41A 3NGQA 3I46A 5A7IA 3N9VA 3MTCA 4QHEA 3G91A 4CMNA 5HT2A 1DE9A 3W2YA 1WDUA 4FVAA 5CFGA 5EWTA 1NTFA 3G2DA 4A9CA 4B5IA 3G0AA 3K55A 3U8UA 3DNIA 5DV2A 3G38A 1HD7A 2ISIA 4F1IA 4QH9A 3WCXA 4L21A 2A42B 5DG0A 1DEWA 2DDSA 2EI9A 2UYRX 3I5VA 4FPVA 3G8VA 4B5FA 2D1KB 4B5HA 2F1NA 3L1WA 1DE8A 3G1KA 3G6SA 4JG3A 4L1YA 3TEBA 2A40B 3NGOA 2J63A 5DFJA 5DFIA 3I48A 3NGNA 4GZ0A 1VYBA 2V0RA 1BIXA 3G4TA 2V0SA 1DNKA 3G00A 1ZWXA 5J3SA 5J3ZA 4B5MA 1I9ZA 5A7JA 5INOA 2IMQX 2DNJA 3GA6A 1SR4B 5J8NA 2XSWA 1Y21A 3NR8A 5INMA 3G3YA 5INLA 4GEWA 3G3CA 1SI6X 4C1RA 5INQA 1ATND 2A41B 4PUQA 5J42A 4B5JA 2O3CA 4QHDA 5CFEA 5DFFA 5DV4A 4B5GA 4RUWA 4F1HA 2DDTA 4L1ZA 1E9NA 1I9YA 3W2XA 2VOAA 4F1RA 2F2FB 4CMLA 2JC4A 3CJCD 3FZIA 4LNDA 5INPA 2DDRA 1YJHA 4F1HB 3G0RA 4K6LF 4GYZA 4L20A 5INNA 2O3HA 3G2CA
chains in the Genus database with same CATH topology
1AKOA 5INKA 5J3PA 5DFHA 4IEMA 4GZ2A 4GZ1A 3MPRA 3W3DB 2A3ZB 4AWNA 2JC5A 3I41A 3NGQA 3I46A 5A7IA 3N9VA 3MTCA 4QHEA 3G91A 4CMNA 5HT2A 1DE9A 3W2YA 1WDUA 4FVAA 5CFGA 5EWTA 1NTFA 3G2DA 4A9CA 4B5IA 3G0AA 3K55A 3U8UA 3DNIA 5DV2A 3G38A 1HD7A 2ISIA 4F1IA 4QH9A 3WCXA 4L21A 2A42B 5DG0A 1DEWA 2DDSA 2EI9A 2UYRX 3I5VA 4FPVA 3G8VA 4B5FA 2D1KB 4B5HA 2F1NA 3L1WA 1DE8A 3G1KA 3G6SA 4JG3A 4L1YA 3TEBA 2A40B 3NGOA 2J63A 5DFJA 5DFIA 3I48A 3NGNA 4GZ0A 1VYBA 2V0RA 1BIXA 3G4TA 2V0SA 1DNKA 3G00A 1ZWXA 5J3SA 5J3ZA 4B5MA 1I9ZA 5A7JA 5INOA 2IMQX 2DNJA 3GA6A 1SR4B 5J8NA 2XSWA 1Y21A 3NR8A 5INMA 3G3YA 5INLA 4GEWA 3G3CA 1SI6X 4C1RA 5INQA 1ATND 2A41B 4PUQA 5J42A 4B5JA 2O3CA 4QHDA 5CFEA 5DFFA 5DV4A 4B5GA 4RUWA 4F1HA 2DDTA 4L1ZA 1E9NA 1I9YA 3W2XA 2VOAA 4F1RA 2F2FB 4CMLA 2JC4A 3CJCD 3FZIA 4LNDA 5INPA 2DDRA 1YJHA 4F1HB 3G0RA 4K6LF 4GYZA 4L20A 5INNA 2O3HA 3G2CA
chains in the Genus database with same CATH homology


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