4NDHA

Human aprataxin (aptx) bound to dna, amp, and zn - product complex
Total Genus 56
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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
56
sequence length
180
structure length
180
Chain Sequence
GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW
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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 Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.
pubmed doi rcsb
molecule tags Dna binding protein/dna
source organism Homo sapiens
molecule keywords Aprataxin
total genus 56
structure length 180
sequence length 180
chains with identical sequence B
ec nomenclature ec 3.1.11.7: Adenosine-5'-diphospho-5'-(DNA) diphosphatase.
pdb deposition date 2013-10-26

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF11969 DcpS_C Scavenger mRNA decapping enzyme C-term binding
A PF16278 zf-C2HE C2HE / C2H2 / C2HC zinc-binding finger
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.428.10 Alpha Beta 2-Layer Sandwich HIT family, subunit A HIT-like 4ndhA00
2FITA 1Z84A 5I2FA 3IMIA 2Q4HA 3I24A 1KPBA 3P0TA 1VLRA 4XBAA 4NDGA 1FHIA 3SZQA 3I4SA 5ED3A 3O1ZA 5CS2A 4QEBA 1KPAA 1AV5A 4NJYA 1ST4A 4ZKLA 5IPDA 3L7XA 4RHNA 1HXPA 5BV3A 3OHEA 3O1XA 5FITA 3O0MA 3R6FA 3ANOA 5RHNA 3N1SA 4INCA 1ZWJA 4INIA 5IPEA 3N1TA 3WO5A 5IN3A 1XMMA 1HXQA 4EGUA 4NJZA 3TW2A 3SPLA 1Y23A 4EQGA 3BLAA 4EQEA 1EMSA 4ZKVA 4YKLB 3FITA 6FITA 1RZYA 4NDHA 4NDIA 3OJ7A 2Q4LA 4ZGLA 1GUQA 5EMTA 3SPDA 2FHIA 3BL9A 1ST0A 4QDEA 4FITA 3OXKA 1KPCA 4EQHA 5IPBA 2OIKA 4NDFA 3O1CA 4QDVA 3SP4A 4NJXA 1KPEA 4NK0A 3KSVA 3NRDA 1FITA 5ED6A 3RHNA 3LB5A 1GUPA 3QGZA 5I2EA 3OMFA 5IPCA 3BL7A 1XMLA 2H39A 6RHNA 2EO4A 1KPFA
chains in the Genus database with same CATH superfamily
2FITA 2R8FA 1Z84A 5I2FA 3IMIA 2Q4HA 3I24A 1KPBA 3P0TA 1VLRA 4XBAA 4NDGA 1FHIA 3SZQA 3I4SA 4G0JA 5ED3A 3O1ZA 5CS2A 4QEBA 1KPAA 1AV5A 4NJYA 1ST4A 4ZKLA 5IPDA 3L7XA 4RHNA 1HXPA 5BV3A 3OHEA 3O1XA 1L9VA 2GU0A 5FITA 4G0AA 3O0MA 3R6FA 3ANOA 5RHNA 3N1SA 2R7PA 4INCA 1ZWJA 4INIA 5IPEA 3N1TA 3WO5A 5IN3A 1XMMA 1HXQA 4EGUA 4NJZA 3TW2A 3SPLA 1Y23A 4EQGA 3BLAA 4EQEA 1EMSA 4ZKVA 4YKLB 2R7JA 3FITA 6FITA 1RZYA 2LJWA 4NDHA 4NDIA 3OJ7A 2Q4LA 4ZGLA 1GUQA 5EMTA 3SPDA 2FHIA 3BL9A 2POFA 1ST0A 4QDEA 4FITA 3OXKA 1KPCA 4EQHA 5IPBA 2OIKA 4NDFA 2R7CA 3O1CA 4QDVA 3SP4A 4NJXA 1KPEA 4NK0A 3KSVA 4I5VA 3NRDA 1FITA 4I5TA 5ED6A 3LB5A 3RHNA 4I5WA 1GUPA 3QGZA 5I2EA 3OMFA 5IPCA 3BL7A 1XMLA 2H39A 6RHNA 2EO4A 1KPFA
chains in the Genus database with same CATH topology
2FITA 1Z84A 5I2FA 3IMIA 2Q4HA 3I24A 1KPBA 3P0TA 1VLRA 4XBAA 4NDGA 1FHIA 3SZQA 3I4SA 5ED3A 3O1ZA 5CS2A 4QEBA 1KPAA 1AV5A 4NJYA 1ST4A 4ZKLA 5IPDA 3L7XA 4RHNA 1HXPA 5BV3A 3OHEA 3O1XA 5FITA 3O0MA 3R6FA 3ANOA 5RHNA 3N1SA 4INCA 1ZWJA 4INIA 5IPEA 3N1TA 3WO5A 5IN3A 1XMMA 1HXQA 4EGUA 4NJZA 3TW2A 3SPLA 1Y23A 4EQGA 3BLAA 4EQEA 1EMSA 4ZKVA 4YKLB 3FITA 6FITA 1RZYA 4NDHA 4NDIA 3OJ7A 2Q4LA 4ZGLA 1GUQA 5EMTA 3SPDA 2FHIA 3BL9A 1ST0A 4QDEA 4FITA 3OXKA 1KPCA 4EQHA 5IPBA 2OIKA 4NDFA 3O1CA 4QDVA 3SP4A 4NJXA 1KPEA 4NK0A 3KSVA 3NRDA 1FITA 5ED6A 3RHNA 3LB5A 1GUPA 3QGZA 5I2EA 3OMFA 5IPCA 3BL7A 1XMLA 2H39A 6RHNA 2EO4A 1KPFA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2FIT A;  1Z84 A;  5I2F A;  3IMI A;  2Q4H A;  3I24 A;  1KPB A;  3P0T A;  1VLR A;  4XBA A;  4NDG A;  1FHI A;  3SZQ A;  3I4S A;  5ED3 A;  3O1Z A;  5CS2 A;  4QEB A;  1KPA A;  1AV5 A;  4NJY A;  1ST4 A;  4ZKL A;  5IPD A;  3L7X A;  4RHN A;  1HXP A;  5BV3 A;  3OHE A;  3O1X A;  5FIT A;  3O0M A;  3R6F A;  3ANO A;  5RHN A;  3N1S A;  4INC A;  1ZWJ A;  4INI A;  5IPE A;  3N1T A;  3WO5 A;  5IN3 A;  1XMM A;  1HXQ A;  4EGU A;  4NJZ A;  3TW2 A;  3SPL A;  1Y23 A;  4EQG A;  3BLA A;  4EQE A;  1EMS A;  4ZKV A;  4YKL B;  3FIT A;  6FIT A;  1RZY A;  4NDH A;  4NDI A;  3OJ7 A;  2Q4L A;  4ZGL A;  1GUQ A;  5EMT A;  3SPD A;  2FHI A;  3BL9 A;  1ST0 A;  4QDE A;  4FIT A;  3OXK A;  1KPC A;  4EQH A;  5IPB A;  2OIK A;  4NDF A;  3O1C A;  4QDV A;  3SP4 A;  4NJX A;  1KPE A;  4NK0 A;  3KSV A;  3NRD A;  1FIT A;  5ED6 A;  3RHN A;  3LB5 A;  1GUP A;  3QGZ A;  5I2E A;  3OMF A;  5IPC A;  3BL7 A;  1XML A;  2H39 A;  6RHN A;  2EO4 A;  1KPF A; 
#chains in the Genus database with same CATH topology
 2FIT A;  2R8F A;  1Z84 A;  5I2F A;  3IMI A;  2Q4H A;  3I24 A;  1KPB A;  3P0T A;  1VLR A;  4XBA A;  4NDG A;  1FHI A;  3SZQ A;  3I4S A;  4G0J A;  5ED3 A;  3O1Z A;  5CS2 A;  4QEB A;  1KPA A;  1AV5 A;  4NJY A;  1ST4 A;  4ZKL A;  5IPD A;  3L7X A;  4RHN A;  1HXP A;  5BV3 A;  3OHE A;  3O1X A;  1L9V A;  2GU0 A;  5FIT A;  4G0A A;  3O0M A;  3R6F A;  3ANO A;  5RHN A;  3N1S A;  2R7P A;  4INC A;  1ZWJ A;  4INI A;  5IPE A;  3N1T A;  3WO5 A;  5IN3 A;  1XMM A;  1HXQ A;  4EGU A;  4NJZ A;  3TW2 A;  3SPL A;  1Y23 A;  4EQG A;  3BLA A;  4EQE A;  1EMS A;  4ZKV A;  4YKL B;  2R7J A;  3FIT A;  6FIT A;  1RZY A;  2LJW A;  4NDH A;  4NDI A;  3OJ7 A;  2Q4L A;  4ZGL A;  1GUQ A;  5EMT A;  3SPD A;  2FHI A;  3BL9 A;  2POF A;  1ST0 A;  4QDE A;  4FIT A;  3OXK A;  1KPC A;  4EQH A;  5IPB A;  2OIK A;  4NDF A;  2R7C A;  3O1C A;  4QDV A;  3SP4 A;  4NJX A;  1KPE A;  4NK0 A;  3KSV A;  4I5V A;  3NRD A;  1FIT A;  4I5T A;  5ED6 A;  3LB5 A;  3RHN A;  4I5W A;  1GUP A;  3QGZ A;  5I2E A;  3OMF A;  5IPC A;  3BL7 A;  1XML A;  2H39 A;  6RHN A;  2EO4 A;  1KPF A; 
#chains in the Genus database with same CATH homology
 2FIT A;  1Z84 A;  5I2F A;  3IMI A;  2Q4H A;  3I24 A;  1KPB A;  3P0T A;  1VLR A;  4XBA A;  4NDG A;  1FHI A;  3SZQ A;  3I4S A;  5ED3 A;  3O1Z A;  5CS2 A;  4QEB A;  1KPA A;  1AV5 A;  4NJY A;  1ST4 A;  4ZKL A;  5IPD A;  3L7X A;  4RHN A;  1HXP A;  5BV3 A;  3OHE A;  3O1X A;  5FIT A;  3O0M A;  3R6F A;  3ANO A;  5RHN A;  3N1S A;  4INC A;  1ZWJ A;  4INI A;  5IPE A;  3N1T A;  3WO5 A;  5IN3 A;  1XMM A;  1HXQ A;  4EGU A;  4NJZ A;  3TW2 A;  3SPL A;  1Y23 A;  4EQG A;  3BLA A;  4EQE A;  1EMS A;  4ZKV A;  4YKL B;  3FIT A;  6FIT A;  1RZY A;  4NDH A;  4NDI A;  3OJ7 A;  2Q4L A;  4ZGL A;  1GUQ A;  5EMT A;  3SPD A;  2FHI A;  3BL9 A;  1ST0 A;  4QDE A;  4FIT A;  3OXK A;  1KPC A;  4EQH A;  5IPB A;  2OIK A;  4NDF A;  3O1C A;  4QDV A;  3SP4 A;  4NJX A;  1KPE A;  4NK0 A;  3KSV A;  3NRD A;  1FIT A;  5ED6 A;  3RHN A;  3LB5 A;  1GUP A;  3QGZ A;  5I2E A;  3OMF A;  5IPC A;  3BL7 A;  1XML A;  2H39 A;  6RHN A;  2EO4 A;  1KPF 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)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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