1YJ5C

Molecular architecture of mammalian polynucleotide kinase, a dna repair enzyme
Total Genus 14
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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
14
sequence length
105
structure length
105
Chain Sequence
SRGRLWLQSPTGGPPPIFLPSDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVHELKPGLSGSLSLGDVLYLVNGLYPLTLRWEELS
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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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molecule tags Transferase
molecule keywords 5' polynucleotide kinase-3' phosphatase catalytic domain
publication title The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
pubmed doi rcsb
source organism Mus musculus
total genus 14
structure length 105
sequence length 105
ec nomenclature ec 2.7.1.78: Polynucleotide 5'-hydroxyl-kinase.
pdb deposition date 2005-01-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
C PF17913 FHA_2 FHA domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.60.200.20 Mainly Beta Sandwich Tumour Suppressor Smad4 Tumour Suppressor Smad4 1yj5C00
1LGPA 3PO8A 2KFUA 1UHTA 2EH0A 2AFFA 1K2NA 3MDBA 1DMZA 1GXCA 3ELVA 1K3NA 3UNNA 2JQJA 1FHRA 3UV0A 1K2MA 1YJMA 3VA4A 3I6UA 1QU5A 3UN0A 1K3QA 2BRFA 1K3JA 1J4OA 1UJXA 2CSWA 4A0EA 2JQLA 2G1LA 2JQIA 3I6WA 3FM8A 3HUFA 3ELSA 4H87A 3UMZA 1YJ5C 2W3OA 1WLNA 3HUEA 3HX1A 2KB4A 3VPYA 4D9VA 3I0NA 1J4KA 2JKDA 3GQSA 4EGXA 2A0TA 3OUNA 1J4QA 3POAA 2JPEA 2FEZA 2KKLA 2KB3A 5E50A 2PIEA 4EJQA 1G3GA 1R21A 4G2SA 1J4LA 3I0MA 3UOTA 1MZKA 3VA1A 3KT9A 1WV3A 2XT9B 1FHQA 1G6GA 4QCJA 5DJOA 2FF4A 1LGQA 5A8IA 1J4PA 4JONA 2LC1A 3UNMA
chains in the Genus database with same CATH superfamily
5DHRA 1LGPA 1J2FA 5DHTA 3PO8A 1ZOQA 2KFUA 1UHTA 2EH0A 3PFNA 5DHUA 2AFFA 1K2NA 3MDBA 1DMZA 1GXCA 2QV7A 3ELVA 2JGRA 3V7YA 3UNNA 1K3NA 3S40A 2JQJA 1FHRA 1YGSA 3UV0A 5JERA 1K2MA 1YJMA 1Z0SA 4L02A 3VA4A 3I6UA 3A77A 1QU5A 3VZBA 1U7FB 1G88A 3UN0A 3VZDA 2I2AA 1K3QA 2I2CA 2BRFA 1MR1A 3AFOA 3V8QA 1K3JA 4HAOA 1J4OA 3V7UA 1UJXA 2CSWA 5EJFA 4A0EA 4V24A 4JIVD 4KU0D 2JQLA 1U0RA 2G1LA 1U0TA 2JQIA 3I6WA 3FM8A 5JEOA 5EJGA 1U7VA 2P1RA 3HUFA 1DEVA 3ELSA 4H87A 3UMZA 1YJ5C 2I1WA 2W3OA 1WLNA 3HUEA 3HX1A 3V80A 5C4VA 2QVLA 2KB4A 3VPYA 5DHPA 4D9VA 5JEKA 2AN1A 1KHXA 3I0NA 1KHUA 4DY6A 5DHQA 1J4KA 1SUWA 2I2FA 2JKDA 2I2BA 1QWTA 1Z0UA 3GQSA 1U7FA 3T5PA 3V8MA 3V8PA 2Q5FA 4EGXA 2I2DA 3VZCA 2A0TA 4JIWD 3OUNA 1J4QA 3POAA 1Y3HA 2JPEA 5EJHA 4WERA 4A4YA 2FEZA 3V8NA 3DSHA 4WRRA 2KKLA 2KB3A 5E50A 2PIEA 5JEMA 3GMJA 1DD1A 1Z0ZA 4EJQA 3V8RA 2BONA 1R21A 4G2SA 1G3GA 1J4LA 3I0MA 5EJIA 3UOTA 1MZKA 1YT5A 3VA1A 2I29A 1Y3IA 1MK2A 3KT9A 1WV3A 2XT9B 3V7WA 5JELA 1G6GA 4QCJA 5DJOA 1FHQA 2XXSA 3DITA 2FF4A 5BVIA 1LGQA 5JEJA 5A8IA 1U7VB 1J4PA 4JONA 5DHSA 2LC1A 4R9PA 1MJSA 3UNMA
chains in the Genus database with same CATH topology
1LGPA 1J2FA 3PO8A 1ZOQA 2KFUA 1UHTA 2EH0A 2AFFA 1K2NA 3MDBA 1DMZA 1GXCA 2QV7A 3ELVA 2JGRA 3UNNA 1K3NA 3S40A 2JQJA 1FHRA 1YGSA 3UV0A 5JERA 1K2MA 1YJMA 4L02A 3VA4A 3I6UA 3A77A 1QU5A 3VZBA 1U7FB 1G88A 3UN0A 3VZDA 1K3QA 2BRFA 1MR1A 1K3JA 1J4OA 1UJXA 2CSWA 4A0EA 4V24A 4JIVD 4KU0D 2JQLA 2G1LA 2JQIA 3I6WA 3FM8A 5JEOA 1U7VA 2P1RA 3HUFA 1DEVA 3ELSA 4H87A 3UMZA 1YJ5C 2W3OA 1WLNA 3HUEA 3HX1A 5C4VA 2QVLA 2KB4A 3VPYA 4D9VA 5JEKA 1KHXA 3I0NA 1KHUA 1J4KA 2JKDA 1QWTA 3GQSA 1U7FA 3T5PA 4EGXA 3VZCA 2A0TA 4JIWD 3OUNA 1J4QA 3POAA 2JPEA 4WERA 4A4YA 2FEZA 3DSHA 4WRRA 2KKLA 2KB3A 5E50A 2PIEA 5JEMA 3GMJA 1DD1A 4EJQA 2BONA 1R21A 4G2SA 1G3GA 1J4LA 3I0MA 3UOTA 1MZKA 3VA1A 1MK2A 3KT9A 1WV3A 2XT9B 5JELA 1FHQA 1G6GA 4QCJA 5DJOA 2XXSA 3DITA 2FF4A 5BVIA 1LGQA 5JEJA 5A8IA 1U7VB 1J4PA 4JONA 2LC1A 4R9PA 1MJSA 3UNMA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1LGP A;  3PO8 A;  2KFU A;  1UHT A;  2EH0 A;  2AFF A;  1K2N A;  3MDB A;  1DMZ A;  1GXC A;  3ELV A;  1K3N A;  3UNN A;  2JQJ A;  1FHR A;  3UV0 A;  1K2M A;  1YJM A;  3VA4 A;  3I6U A;  1QU5 A;  3UN0 A;  1K3Q A;  2BRF A;  1K3J A;  1J4O A;  1UJX A;  2CSW A;  4A0E A;  2JQL A;  2G1L A;  2JQI A;  3I6W A;  3FM8 A;  3HUF A;  3ELS A;  4H87 A;  3UMZ A;  1YJ5 C;  2W3O A;  1WLN A;  3HUE A;  3HX1 A;  2KB4 A;  3VPY A;  4D9V A;  3I0N A;  1J4K A;  2JKD A;  3GQS A;  4EGX A;  2A0T A;  3OUN A;  1J4Q A;  3POA A;  2JPE A;  2FEZ A;  2KKL A;  2KB3 A;  5E50 A;  2PIE A;  4EJQ A;  1G3G A;  1R21 A;  4G2S A;  1J4L A;  3I0M A;  3UOT A;  1MZK A;  3VA1 A;  3KT9 A;  1WV3 A;  2XT9 B;  1FHQ A;  1G6G A;  4QCJ A;  5DJO A;  2FF4 A;  1LGQ A;  5A8I A;  1J4P A;  4JON A;  2LC1 A;  3UNM A; 
#chains in the Genus database with same CATH topology
 5DHR A;  1LGP A;  1J2F A;  5DHT A;  3PO8 A;  1ZOQ A;  2KFU A;  1UHT A;  2EH0 A;  3PFN A;  5DHU A;  2AFF A;  1K2N A;  3MDB A;  1DMZ A;  1GXC A;  2QV7 A;  3ELV A;  2JGR A;  3V7Y A;  3UNN A;  1K3N A;  3S40 A;  2JQJ A;  1FHR A;  1YGS A;  3UV0 A;  5JER A;  1K2M A;  1YJM A;  1Z0S A;  4L02 A;  3VA4 A;  3I6U A;  3A77 A;  1QU5 A;  3VZB A;  1U7F B;  1G88 A;  3UN0 A;  3VZD A;  2I2A A;  1K3Q A;  2I2C A;  2BRF A;  1MR1 A;  3AFO A;  3V8Q A;  1K3J A;  4HAO A;  1J4O A;  3V7U A;  1UJX A;  2CSW A;  5EJF A;  4A0E A;  4V24 A;  4JIV D;  4KU0 D;  2JQL A;  1U0R A;  2G1L A;  1U0T A;  2JQI A;  3I6W A;  3FM8 A;  5JEO A;  5EJG A;  1U7V A;  2P1R A;  3HUF A;  1DEV A;  3ELS A;  4H87 A;  3UMZ A;  1YJ5 C;  2I1W A;  2W3O A;  1WLN A;  3HUE A;  3HX1 A;  3V80 A;  5C4V A;  2QVL A;  2KB4 A;  3VPY A;  5DHP A;  4D9V A;  5JEK A;  2AN1 A;  1KHX A;  3I0N A;  1KHU A;  4DY6 A;  5DHQ A;  1J4K A;  1SUW A;  2I2F A;  2JKD A;  2I2B A;  1QWT A;  1Z0U A;  3GQS A;  1U7F A;  3T5P A;  3V8M A;  3V8P A;  2Q5F A;  4EGX A;  2I2D A;  3VZC A;  2A0T A;  4JIW D;  3OUN A;  1J4Q A;  3POA A;  1Y3H A;  2JPE A;  5EJH A;  4WER A;  4A4Y A;  2FEZ A;  3V8N A;  3DSH A;  4WRR A;  2KKL A;  2KB3 A;  5E50 A;  2PIE A;  5JEM A;  3GMJ A;  1DD1 A;  1Z0Z A;  4EJQ A;  3V8R A;  2BON A;  1R21 A;  4G2S A;  1G3G A;  1J4L A;  3I0M A;  5EJI A;  3UOT A;  1MZK A;  1YT5 A;  3VA1 A;  2I29 A;  1Y3I A;  1MK2 A;  3KT9 A;  1WV3 A;  2XT9 B;  3V7W A;  5JEL A;  1G6G A;  4QCJ A;  5DJO A;  1FHQ A;  2XXS A;  3DIT A;  2FF4 A;  5BVI A;  1LGQ A;  5JEJ A;  5A8I A;  1U7V B;  1J4P A;  4JON A;  5DHS A;  2LC1 A;  4R9P A;  1MJS A;  3UNM A; 
#chains in the Genus database with same CATH homology
 1LGP A;  1J2F A;  3PO8 A;  1ZOQ A;  2KFU A;  1UHT A;  2EH0 A;  2AFF A;  1K2N A;  3MDB A;  1DMZ A;  1GXC A;  2QV7 A;  3ELV A;  2JGR A;  3UNN A;  1K3N A;  3S40 A;  2JQJ A;  1FHR A;  1YGS A;  3UV0 A;  5JER A;  1K2M A;  1YJM A;  4L02 A;  3VA4 A;  3I6U A;  3A77 A;  1QU5 A;  3VZB A;  1U7F B;  1G88 A;  3UN0 A;  3VZD A;  1K3Q A;  2BRF A;  1MR1 A;  1K3J A;  1J4O A;  1UJX A;  2CSW A;  4A0E A;  4V24 A;  4JIV D;  4KU0 D;  2JQL A;  2G1L A;  2JQI A;  3I6W A;  3FM8 A;  5JEO A;  1U7V A;  2P1R A;  3HUF A;  1DEV A;  3ELS A;  4H87 A;  3UMZ A;  1YJ5 C;  2W3O A;  1WLN A;  3HUE A;  3HX1 A;  5C4V A;  2QVL A;  2KB4 A;  3VPY A;  4D9V A;  5JEK A;  1KHX A;  3I0N A;  1KHU A;  1J4K A;  2JKD A;  1QWT A;  3GQS A;  1U7F A;  3T5P A;  4EGX A;  3VZC A;  2A0T A;  4JIW D;  3OUN A;  1J4Q A;  3POA A;  2JPE A;  4WER A;  4A4Y A;  2FEZ A;  3DSH A;  4WRR A;  2KKL A;  2KB3 A;  5E50 A;  2PIE A;  5JEM A;  3GMJ A;  1DD1 A;  4EJQ A;  2BON A;  1R21 A;  4G2S A;  1G3G A;  1J4L A;  3I0M A;  3UOT A;  1MZK A;  3VA1 A;  1MK2 A;  3KT9 A;  1WV3 A;  2XT9 B;  5JEL A;  1FHQ A;  1G6G A;  4QCJ A;  5DJO A;  2XXS A;  3DIT A;  2FF4 A;  5BVI A;  1LGQ A;  5JEJ A;  5A8I A;  1U7V B;  1J4P A;  4JON A;  2LC1 A;  4R9P A;  1MJS A;  3UNM 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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