5DFIA

Human ape1 phosphorothioate substrate complex
Total Genus 88

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
88
sequence length
276
structure length
276
Chain Sequence
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

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
EMPTYTVIII1 (89-92)TII1 (125-128)AH2 (80-87)TI1 (54-57)S1 (62-68)AH1 (72-78)TIV1 (69-72)TI2 (111-114)S2 (91-95)TIV2 (94-97)3H1 (101-103)S3 (116-120)TIV3 (112-115)3H2 (106-109)S5 (141-144)S6 (157-162)TI3 (122-125)TI4 (162-165)TIV4 (123-126)S7 (165-171)S4 (131-135)TVIII3 (139-142)TVIII2 (135-138)TIV5 (145-148)AH4 (234-247)AH3 (181-201)S8 (205-210)AH5 (252-256)TI5 (222-225)TI6 (223-226)TI7 (226-229)TII2 (229-232)TIV9 (230-233)TI8 (257-260)TIV10 (260-263)3H4 (177-179)3H5 (217-219)TIV7 (220-223)S9 (249-251)TII3 (269-272)3H3 (149-151)3H6 (273-276)Updating...
connected with : NaN
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 88
structure length 276
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
ClassArchitectureTopologyHomologyDomain
3.60.10.10 Alpha Beta 4-Layer Sandwich Deoxyribonuclease I; Chain A Endonuclease/exonuclease/phosphatase 5dfiA00
1DNKA 2JC4A 3L1WA 4FPVA 4B5FA 3FZIA 4CMLA 5DFJA 4QHEA 2V0RA 3G4TA 3CJCD 5A7JA 5INNA 5HT2A 5CFEA 2IMQX 2A42B 2DNJA 1AKOA 1I9YA 4CMNA 2A40B 5DV4A 3G3YA 4QHDA 5INKA 4B5MA 4JG3A 4C1RA 2V0SA 2F1NA 2F2FB 4FVAA 1I9ZA 5INOA 4A9CA 4L20A 4QH9A 4GEWA 1YJHA 3NGNA 4AWNA 4GZ0A 1DEWA 3G2CA 5DV2A 4K6LF 4PUQA 3W2YA 3G6SA 4GYZA 3U8UA 5DG0A 1VYBA 4F1HA 3G3CA 1ZWXA 3TEBA 4L21A 2A3ZB 5DFFA 5EWTA 1BIXA 1NTFA 3I41A 3I46A 4LNDA 5J3PA 3GA6A 4B5HA 2UYRX 5INPA 3G2DA 1HD7A 5DFHA 2DDSA 1ATND 5INLA 2O3CA 4B5GA 3G91A 2D1KB 3NGOA 3G8VA 5INMA 1SR4B 4RUWA 3N9VA 5J8NA 5J42A 5INQA 5DFIA 3I5VA 2A41B 3G0AA 5A7IA 3W3DB 3G1KA 2VOAA 4B5JA 2ISIA 3G00A 5J3ZA 4L1ZA 2J63A 3MPRA 1SI6X 1WDUA 3NGQA 4GZ2A 2DDTA 5CFGA 3K55A 4IEMA 2EI9A 3G38A 1DE9A 5J3SA 3NR8A 3G0RA 3WCXA 3I48A 4L1YA 2XSWA 3W2XA 1Y21A 4B5IA 4F1RA 3MTCA 1DE8A 1E9NA 3DNIA 4F1IA 4GZ1A 2O3HA 4F1HB 2DDRA 2JC5A
chains in the Genus database with same CATH superfamily
1DNKA 2JC4A 3L1WA 4FPVA 4B5FA 3FZIA 4CMLA 5DFJA 4QHEA 2V0RA 3G4TA 3CJCD 5A7JA 5INNA 5HT2A 5CFEA 2IMQX 2A42B 2DNJA 1AKOA 1I9YA 4CMNA 2A40B 5DV4A 3G3YA 4QHDA 5INKA 4B5MA 4JG3A 4C1RA 2V0SA 2F1NA 2F2FB 4FVAA 1I9ZA 5INOA 4A9CA 4L20A 4QH9A 4GEWA 1YJHA 3NGNA 4AWNA 4GZ0A 1DEWA 3G2CA 5DV2A 4K6LF 4PUQA 3W2YA 3G6SA 4GYZA 3U8UA 5DG0A 1VYBA 4F1HA 3G3CA 1ZWXA 3TEBA 4L21A 2A3ZB 5DFFA 5EWTA 1BIXA 1NTFA 3I41A 3I46A 4LNDA 5J3PA 3GA6A 4B5HA 2UYRX 5INPA 3G2DA 1HD7A 5DFHA 2DDSA 1ATND 5INLA 2O3CA 4B5GA 3G91A 2D1KB 3NGOA 3G8VA 5INMA 1SR4B 4RUWA 3N9VA 5J8NA 5J42A 5INQA 5DFIA 3I5VA 2A41B 3G0AA 5A7IA 3W3DB 3G1KA 2VOAA 4B5JA 2ISIA 3G00A 5J3ZA 4L1ZA 2J63A 3MPRA 1SI6X 1WDUA 3NGQA 4GZ2A 2DDTA 5CFGA 3K55A 4IEMA 2EI9A 3G38A 1DE9A 5J3SA 3NR8A 3G0RA 3WCXA 3I48A 4L1YA 2XSWA 3W2XA 1Y21A 4B5IA 4F1RA 3MTCA 1DE8A 1E9NA 3DNIA 4F1IA 4GZ1A 2O3HA 4F1HB 2DDRA 2JC5A
chains in the Genus database with same CATH topology
1DNKA 2JC4A 3L1WA 4FPVA 4B5FA 3FZIA 4CMLA 5DFJA 4QHEA 2V0RA 3G4TA 3CJCD 5A7JA 5INNA 5HT2A 5CFEA 2IMQX 2A42B 2DNJA 1AKOA 1I9YA 4CMNA 2A40B 5DV4A 3G3YA 4QHDA 5INKA 4B5MA 4JG3A 4C1RA 2V0SA 2F1NA 2F2FB 4FVAA 1I9ZA 5INOA 4A9CA 4L20A 4QH9A 4GEWA 1YJHA 3NGNA 4AWNA 4GZ0A 1DEWA 3G2CA 5DV2A 4K6LF 4PUQA 3W2YA 3G6SA 4GYZA 3U8UA 5DG0A 1VYBA 4F1HA 3G3CA 1ZWXA 3TEBA 4L21A 2A3ZB 5DFFA 5EWTA 1BIXA 1NTFA 3I41A 3I46A 4LNDA 5J3PA 3GA6A 4B5HA 2UYRX 5INPA 3G2DA 1HD7A 5DFHA 2DDSA 1ATND 5INLA 2O3CA 4B5GA 3G91A 2D1KB 3NGOA 3G8VA 5INMA 1SR4B 4RUWA 3N9VA 5J8NA 5J42A 5INQA 5DFIA 3I5VA 2A41B 3G0AA 5A7IA 3W3DB 3G1KA 2VOAA 4B5JA 2ISIA 3G00A 5J3ZA 4L1ZA 2J63A 3MPRA 1SI6X 1WDUA 3NGQA 4GZ2A 2DDTA 5CFGA 3K55A 4IEMA 2EI9A 3G38A 1DE9A 5J3SA 3NR8A 3G0RA 3WCXA 3I48A 4L1YA 2XSWA 3W2XA 1Y21A 4B5IA 4F1RA 3MTCA 1DE8A 1E9NA 3DNIA 4F1IA 4GZ1A 2O3HA 4F1HB 2DDRA 2JC5A
chains in the Genus database with same CATH homology


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