1UM2A

Crystal structure of the vma1-derived endonuclease with the ligated extein segment
Total Genus 90

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
90
sequence length
454
structure length
417
Chain Sequence
SFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHN
50100150200250300350400400300200100
020406080Genus Matrix

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
EMPTYTI4 (397-400)TI1 (293-296)TII1 (286-289)TI3 (359-362)TIV1 (300-303)TIV2 (312-315)S1 (308-311)TI2 (301-304)S5 (363-369)TII2 (305-308)S2 (317-320)S3 (325-335)S7 (377-379)TIV3 (378-381)S4 (355-359)S8 (382-396)TIV5 (414-417)S9 (402-414)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Saccharomyces cerevisiae
publication title Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.
pubmed rcsb
molecule keywords ENDONUCLEASE PI-SCEI
total genus 90
structure length 417
sequence length 454
chains with identical sequence B
ec nomenclature ec 7.1.2.2: H(+)-transporting two-sector ATPase.
pdb deposition date 2003-09-22

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF05203 Hom_end_hint Hom_end-associated Hint
A PF05204 Hom_end Homing endonuclease
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.170.16.10 Mainly Beta Beta Complex Endonuclease - Pi-scei; Chain A, domain 1 Hedgehog/Intein (Hint) domain 1um2A01
3.10.28.10 Alpha Beta Roll Endonuclease I-creI Homing endonucleases 1um2A02
3.10.28.10 Alpha Beta Roll Endonuclease I-creI Homing endonucleases 1um2A03
4O1SA 1LWSA 2VS8A 1U0DA 5A74A 4AQXA 3MXBA 2VBLA 5E67A 4UN9G 4UN7G 2IN8A 1BP7A 3C0WA 1T9IA 4GIGA 5A0MB 2VBNB 2IMZA 1B24A 4UN9A 4Z1ZA 4UN7A 5E5OA 3FD2A 3IGDA 3KO2A 5AK9A 1G9YA 4O1RA 4LOXA 2VS7A 2I3QA 3QQYA 2LQMA 4UNCA 1VDEA 3HYIA 3MXBB 1AF5A 1ZD7A 2XE0B 2VBLB 4UNAA 2IN9A 1M5XA 2LWYA 2VBOB 2XE0A 3E54A 5AKNA 3MIPA 4UT0A 4E2TA 3HYJA 1AM2A 1T9JA 2VBJA 2LCJA 2JNQA 4D6OA 2VBOA 1ZDEA 1G9ZA 1DQ3A 4UN8G 1R7MA 3C0XA 1DFAA 4KL5A 5A0WA 4UN8A 3IFJA 1GPPA 4YITA 4LQ0A 4EFJA 1UM2A 2VBJB 4Z1XA 4AQUA 3MX9A 2AB5A 1JVAA 4UNBA 2JMZA 4Z20A 2DCHX 5K08A 3MISA 4E2UA 4AAGA 2FLDA 4OZ6A 1N3EA 3OOLA 5AKMA 1MI8A 1LWTA 2QOJZ 1MOWA 2I3PA 2L8LA 1AT0A 3NZMA 1U0CA 2O7MA 1EF0A 5A77A 2CW7A 2EX5A 4AABA 5A78A 3R7PA 5I0AA 4KL6A 3MXAA 3EH8A 4AAEA 2KEQA 5E5SA 4YHXA 2IN0A 5E63A 4AAFA 5A0MA 2VBNA 1P8KZ 3OORA 1N3FA 5AKFA 5A72A 4YISA 4AADA 2CW8A 3UVFA 4D6NA
chains in the Genus database with same CATH superfamily
4O1SA 1LWSA 2VS8A 1U0DA 5A74A 4AQXA 3MXBA 4KZSA 2VBLA 5E67A 4UN9G 4UN7G 2IN8A 1BP7A 3C0WA 1T9IA 4GIGA 5A0MB 2VBNB 2IMZA 1B24A 4UN9A 4Z1ZA 4UN7A 5E5OA 3FD2A 3IGDA 3KO2A 5AK9A 1G9YA 4O1RA 4LOXA 2VS7A 2I3QA 3QQYA 2LQMA 4UNCA 1VDEA 3HYIA 3MXBB 1AF5A 1ZD7A 2XE0B 2VBLB 4UNAA 2IN9A 1M5XA 2LWYA 2VBOB 2XE0A 3E54A 5AKNA 3MIPA 4UT0A 4E2TA 3HYJA 1AM2A 1T9JA 2VBJA 2LCJA 2JNQA 4D6OA 2VBOA 1ZDEA 1G9ZA 1DQ3A 4UN8G 1R7MA 3C0XA 1DFAA 4KL5A 5A0WA 4UN8A 3IFJA 1GPPA 4YITA 4LQ0A 4EFJA 1UM2A 2VBJB 4Z1XA 4AQUA 3MX9A 2AB5A 1JVAA 4UNBA 2JMZA 4Z20A 2DCHX 5K08A 3MISA 4E2UA 4AAGA 2FLDA 4OZ6A 1N3EA 3OOLA 5AKMA 1MI8A 1LWTA 2QOJZ 1MOWA 2I3PA 2L8LA 1AT0A 3NZMA 1U0CA 2O7MA 1EF0A 5A77A 2CW7A 2EX5A 4LX3A 4AABA 5A78A 3R7PA 5I0AA 4KL6A 3MXAA 3EH8A 4AAEA 2KEQA 5E5SA 4YHXA 4QFQA 2IN0A 5E63A 4AAFA 5A0MA 2VBNA 1P8KZ 3OORA 2F4LA 1N3FA 5AKFA 5A72A 4YISA 4AADA 2CW8A 3UVFA 4D6NA
chains in the Genus database with same CATH topology
4O1SA 1LWSA 2VS8A 1U0DA 5A74A 4AQXA 3MXBA 2VBLA 5E67A 4UN9G 4UN7G 2IN8A 1BP7A 3C0WA 1T9IA 4GIGA 5A0MB 2VBNB 2IMZA 1B24A 4UN9A 4Z1ZA 4UN7A 5E5OA 3FD2A 3IGDA 3KO2A 5AK9A 1G9YA 4O1RA 4LOXA 2VS7A 2I3QA 3QQYA 2LQMA 4UNCA 1VDEA 3HYIA 3MXBB 1AF5A 1ZD7A 2XE0B 2VBLB 4UNAA 2IN9A 1M5XA 2LWYA 2VBOB 2XE0A 3E54A 5AKNA 3MIPA 4UT0A 4E2TA 3HYJA 1AM2A 1T9JA 2VBJA 2LCJA 2JNQA 4D6OA 2VBOA 1ZDEA 1G9ZA 1DQ3A 4UN8G 1R7MA 3C0XA 1DFAA 4KL5A 5A0WA 4UN8A 3IFJA 1GPPA 4YITA 4LQ0A 4EFJA 1UM2A 2VBJB 4Z1XA 4AQUA 3MX9A 2AB5A 1JVAA 4UNBA 2JMZA 4Z20A 2DCHX 5K08A 3MISA 4E2UA 4AAGA 2FLDA 4OZ6A 1N3EA 3OOLA 5AKMA 1MI8A 1LWTA 2QOJZ 1MOWA 2I3PA 2L8LA 1AT0A 3NZMA 1U0CA 2O7MA 1EF0A 5A77A 2CW7A 2EX5A 4AABA 5A78A 3R7PA 5I0AA 4KL6A 3MXAA 3EH8A 4AAEA 2KEQA 5E5SA 4YHXA 2IN0A 5E63A 4AAFA 5A0MA 2VBNA 1P8KZ 3OORA 1N3FA 5AKFA 5A72A 4YISA 4AADA 2CW8A 3UVFA 4D6NA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4O1S A;  1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  2IN8 A;  1BP7 A;  3C0W A;  1T9I A;  4GIG A;  5A0M B;  2VBN B;  2IMZ A;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3IGD A;  3KO2 A;  5AK9 A;  1G9Y A;  4O1R A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  2LQM A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  1AF5 A;  1ZD7 A;  2XE0 B;  2VBL B;  4UNA A;  2IN9 A;  1M5X A;  2LWY A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  4E2T A;  3HYJ A;  1AM2 A;  1T9J A;  2VBJ A;  2LCJ A;  2JNQ A;  4D6O A;  2VBO A;  1ZDE A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  4KL5 A;  5A0W A;  4UN8 A;  3IFJ A;  1GPP A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  2JMZ A;  4Z20 A;  2DCH X;  5K08 A;  3MIS A;  4E2U A;  4AAG A;  2FLD A;  4OZ6 A;  1N3E A;  3OOL A;  5AKM A;  1MI8 A;  1LWT A;  2QOJ Z;  1MOW A;  2I3P A;  2L8L A;  1AT0 A;  3NZM A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4AAB A;  5A78 A;  3R7P A;  5I0A A;  4KL6 A;  3MXA A;  3EH8 A;  4AAE A;  2KEQ A;  5E5S A;  4YHX A;  2IN0 A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N A; 
#chains in the Genus database with same CATH topology
 4O1S A;  1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  4KZS A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  2IN8 A;  1BP7 A;  3C0W A;  1T9I A;  4GIG A;  5A0M B;  2VBN B;  2IMZ A;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3IGD A;  3KO2 A;  5AK9 A;  1G9Y A;  4O1R A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  2LQM A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  1AF5 A;  1ZD7 A;  2XE0 B;  2VBL B;  4UNA A;  2IN9 A;  1M5X A;  2LWY A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  4E2T A;  3HYJ A;  1AM2 A;  1T9J A;  2VBJ A;  2LCJ A;  2JNQ A;  4D6O A;  2VBO A;  1ZDE A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  4KL5 A;  5A0W A;  4UN8 A;  3IFJ A;  1GPP A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  2JMZ A;  4Z20 A;  2DCH X;  5K08 A;  3MIS A;  4E2U A;  4AAG A;  2FLD A;  4OZ6 A;  1N3E A;  3OOL A;  5AKM A;  1MI8 A;  1LWT A;  2QOJ Z;  1MOW A;  2I3P A;  2L8L A;  1AT0 A;  3NZM A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4LX3 A;  4AAB A;  5A78 A;  3R7P A;  5I0A A;  4KL6 A;  3MXA A;  3EH8 A;  4AAE A;  2KEQ A;  5E5S A;  4YHX A;  4QFQ A;  2IN0 A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  2F4L A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N A; 
#chains in the Genus database with same CATH homology
 4O1S A;  1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  2IN8 A;  1BP7 A;  3C0W A;  1T9I A;  4GIG A;  5A0M B;  2VBN B;  2IMZ A;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3IGD A;  3KO2 A;  5AK9 A;  1G9Y A;  4O1R A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  2LQM A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  1AF5 A;  1ZD7 A;  2XE0 B;  2VBL B;  4UNA A;  2IN9 A;  1M5X A;  2LWY A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  4E2T A;  3HYJ A;  1AM2 A;  1T9J A;  2VBJ A;  2LCJ A;  2JNQ A;  4D6O A;  2VBO A;  1ZDE A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  4KL5 A;  5A0W A;  4UN8 A;  3IFJ A;  1GPP A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  2JMZ A;  4Z20 A;  2DCH X;  5K08 A;  3MIS A;  4E2U A;  4AAG A;  2FLD A;  4OZ6 A;  1N3E A;  3OOL A;  5AKM A;  1MI8 A;  1LWT A;  2QOJ Z;  1MOW A;  2I3P A;  2L8L A;  1AT0 A;  3NZM A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4AAB A;  5A78 A;  3R7P A;  5I0A A;  4KL6 A;  3MXA A;  3EH8 A;  4AAE A;  2KEQ A;  5E5S A;  4YHX A;  2IN0 A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N A; 
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similar chains in the Genus database (?% sequence similarity)
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