1JVA | Genus

Total Genus 117

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	117
sequence length	460
structure length	427
Chain Sequence	VGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSEVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGER

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

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Hydrolase
source organism	Saccharomyces cerevisiae
publication title	Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides. pubmed doi rcsb
molecule keywords	VMA1-DERIVED HOMING ENDONUCLEASE X10SSS
total genus	117
structure length	427
sequence length	460
chains with identical sequence	B
ec nomenclature	ec 7.1.2.2: H(+)-transporting two-sector ATPase.
pdb deposition date	2001-08-29

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	Class	Architecture	Topology	Homology	Domain
2.170.16.10	Mainly Beta	Beta Complex	Endonuclease - Pi-scei; Chain A, domain 1	Hedgehog/Intein (Hint) domain	1jvaA01
3.10.28.10	Alpha Beta	Roll	Endonuclease I-creI	Homing endonucleases	1jvaA02
3.10.28.10	Alpha Beta	Roll	Endonuclease I-creI	Homing endonucleases	1jvaA03

3R7PA 4Z20A 1DQ3A 4GIGA 2IN9A 4AADA 3EH8A 2LCJA 3MXAA 1UM2A 3HYIA 1N3FA 2VBOB 3IGDA 2FLDA 3QQYA 2KEQA 4OZ6A 1P8KZ 3OORA 2JMZA 2L8LA 2O7MA 4UN7G 3OOLA 5K08A 1BP7A 4YITA 4UNCA 4KL5A 2VS7A 1MOWA 3MX9A 1U0DA 2CW7A 5A77A 3IFJA 4UN9G 4Z1ZA 5A72A 4E2TA 4UT0A 5A78A 4UNBA 2IN0A 1GPPA 4EFJA 5E63A 4O1RA 4UN8G 1EF0A 2JNQA 2EX5A 2QOJZ 1LWTA 3KO2A 2VBNB 3E54A 4UN9A 3MISA 4AQXA 3MIPA 3C0WA 2I3PA 1ZDEA 1ZD7A 4E2UA 5E5SA 4D6OA 1M5XA 4D6NA 3C0XA 2CW8A 5A0MA 1JVAA 1G9ZA 2VBNA 2I3QA 2DCHX 5A74A 4AABA 4LQ0A 4AQUA 4UN7A 2IN8A 2VBJA 2XE0B 1AM2A 5E5OA 5A0MB 2VBLB 5I0AA 1U0CA 1MI8A 5E67A 5AK9A 5AKNA 3MXBB 2AB5A 4KL6A 1AT0A 4O1SA 1LWSA 2VBJB 5AKFA 1T9IA 2XE0A 1VDEA 4UN8A 1T9JA 4YHXA 2VBLA 3HYJA 3MXBA 4AAFA 4AAGA 5A0WA 1AF5A 4UNAA 2VS8A 1DFAA 4AAEA 4YISA 2LQMA 2LWYA 3NZMA 5AKMA 3FD2A 1B24A 4LOXA 1R7MA 1G9YA 2VBOA 1N3EA 2IMZA 3UVFA 4Z1XA
chains in the Genus database with same CATH superfamily

3R7PA 4Z20A 1DQ3A 4GIGA 2IN9A 4AADA 3EH8A 2LCJA 3MXAA 1UM2A 3HYIA 1N3FA 2VBOB 3IGDA 2FLDA 3QQYA 2KEQA 4OZ6A 1P8KZ 3OORA 2JMZA 2L8LA 2O7MA 4UN7G 3OOLA 5K08A 1BP7A 4YITA 4UNCA 4KL5A 2VS7A 1MOWA 3MX9A 1U0DA 2CW7A 5A77A 3IFJA 4UN9G 4Z1ZA 5A72A 4E2TA 4UT0A 5A78A 4UNBA 2IN0A 1GPPA 4EFJA 5E63A 4O1RA 4UN8G 1EF0A 2JNQA 2EX5A 2QOJZ 1LWTA 3KO2A 2VBNB 3E54A 4UN9A 3MISA 4AQXA 3MIPA 3C0WA 2I3PA 1ZDEA 1ZD7A 4E2UA 5E5SA 4D6OA 1M5XA 4D6NA 3C0XA 2CW8A 5A0MA 1JVAA 1G9ZA 2VBNA 2I3QA 2DCHX 5A74A 4AABA 4LQ0A 4KZSA 4UN7A 4AQUA 2IN8A 2VBJA 2XE0B 1AM2A 5E5OA 5A0MB 2VBLB 5I0AA 1U0CA 1MI8A 5E67A 5AK9A 5AKNA 3MXBB 2AB5A 4KL6A 4LX3A 1AT0A 4O1SA 1LWSA 2VBJB 5AKFA 1T9IA 2XE0A 1VDEA 4UN8A 1T9JA 4YHXA 4QFQA 2VBLA 3HYJA 2F4LA 3MXBA 4AAFA 4AAGA 5A0WA 1AF5A 4UNAA 2VS8A 1DFAA 4AAEA 4YISA 2LQMA 2LWYA 3NZMA 5AKMA 3FD2A 1B24A 4LOXA 1R7MA 1G9YA 2VBOA 1N3EA 2IMZA 3UVFA 4Z1XA
chains in the Genus database with same CATH topology

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations