4NDFA

Human aprataxin (aptx) bound to rna-dna, amp, and zn - product complex
Total Genus 55
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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
55
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/rna/dna
source organism Homo sapiens
molecule keywords Aprataxin
total genus 55
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 4ndfA00
4EQEA 6RHNA 4NJXA 2OIKA 3P0TA 1AV5A 3OXKA 5ED6A 4RHNA 5BV3A 1HXQA 1KPBA 1XMLA 3LB5A 3QGZA 3WO5A 4NDHA 3SP4A 4EGUA 3N1TA 3OHEA 1GUQA 3R6FA 4QEBA 3O1ZA 2Q4LA 1ST4A 1KPAA 3BLAA 1KPFA 6FITA 3NRDA 3I24A 3I4SA 4NDGA 5IN3A 3TW2A 2FITA 3OMFA 3BL7A 5IPBA 4FITA 1EMSA 4QDEA 4NJZA 2FHIA 3RHNA 1FHIA 1FITA 3N1SA 4XBAA 3KSVA 5CS2A 1Y23A 5FITA 3O1XA 4YKLB 5IPEA 2H39A 3BL9A 1ZWJA 4NK0A 4QDVA 3SPLA 4INCA 2EO4A 3SPDA 1GUPA 5I2FA 4NDIA 1RZYA 5I2EA 5EMTA 2Q4HA 5IPCA 4ZKLA 4INIA 1KPEA 3FITA 4ZGLA 5IPDA 3O1CA 4NDFA 4ZKVA 1ST0A 1XMMA 3IMIA 4NJYA 1HXPA 3O0MA 1Z84A 5ED3A 1KPCA 4EQHA 3OJ7A 5RHNA 3SZQA 1VLRA 4EQGA 3ANOA 3L7XA
chains in the Genus database with same CATH superfamily
4EQEA 6RHNA 4NJXA 2OIKA 3P0TA 2R7JA 1AV5A 2R8FA 3OXKA 5ED6A 4RHNA 5BV3A 1HXQA 1KPBA 1XMLA 3LB5A 2POFA 3QGZA 3WO5A 4NDHA 3SP4A 4EGUA 3N1TA 2GU0A 3OHEA 1GUQA 3R6FA 4QEBA 3O1ZA 2Q4LA 1ST4A 1KPAA 2R7PA 3BLAA 1KPFA 6FITA 3NRDA 2LJWA 3I24A 3I4SA 4NDGA 5IN3A 3TW2A 2FITA 3OMFA 3BL7A 5IPBA 4I5WA 4FITA 1EMSA 4QDEA 4NJZA 2FHIA 2R7CA 3RHNA 1FHIA 1FITA 3N1SA 4I5TA 4XBAA 3KSVA 5CS2A 1Y23A 5FITA 3O1XA 4YKLB 5IPEA 2H39A 3BL9A 1ZWJA 4NK0A 4QDVA 3SPLA 4INCA 2EO4A 3SPDA 1GUPA 5I2FA 4NDIA 4G0AA 1RZYA 5I2EA 4I5VA 5EMTA 2Q4HA 5IPCA 4ZKLA 4G0JA 4INIA 1KPEA 3FITA 4ZGLA 5IPDA 3O1CA 4NDFA 4ZKVA 1ST0A 1XMMA 3IMIA 4NJYA 1HXPA 3O0MA 1Z84A 5ED3A 1KPCA 4EQHA 3OJ7A 1L9VA 5RHNA 3SZQA 1VLRA 4EQGA 3ANOA 3L7XA
chains in the Genus database with same CATH topology
4EQEA 6RHNA 4NJXA 2OIKA 3P0TA 1AV5A 3OXKA 5ED6A 4RHNA 5BV3A 1HXQA 1KPBA 1XMLA 3LB5A 3QGZA 3WO5A 4NDHA 3SP4A 4EGUA 3N1TA 3OHEA 1GUQA 3R6FA 4QEBA 3O1ZA 2Q4LA 1ST4A 1KPAA 3BLAA 1KPFA 6FITA 3NRDA 3I24A 3I4SA 4NDGA 5IN3A 3TW2A 2FITA 3OMFA 3BL7A 5IPBA 4FITA 1EMSA 4QDEA 4NJZA 2FHIA 3RHNA 1FHIA 1FITA 3N1SA 4XBAA 3KSVA 5CS2A 1Y23A 5FITA 3O1XA 4YKLB 5IPEA 2H39A 3BL9A 1ZWJA 4NK0A 4QDVA 3SPLA 4INCA 2EO4A 3SPDA 1GUPA 5I2FA 4NDIA 1RZYA 5I2EA 5EMTA 2Q4HA 5IPCA 4ZKLA 4INIA 1KPEA 3FITA 4ZGLA 5IPDA 3O1CA 4NDFA 4ZKVA 1ST0A 1XMMA 3IMIA 4NJYA 1HXPA 3O0MA 1Z84A 5ED3A 1KPCA 4EQHA 3OJ7A 5RHNA 3SZQA 1VLRA 4EQGA 3ANOA 3L7XA
chains in the Genus database with same CATH homology


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