3H7KA

Crystal structure of arabidopsis thaliana agmatine deiminase complexed with a covalently bound reaction intermediate
Total Genus 128
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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
128
sequence length
376
structure length
366
Chain Sequence
SEESRESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHITQQQPAEPT
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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 Hydrolase
molecule keywords Agmatine deiminase
publication title Structural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase
rcsb
source organism Arabidopsis thaliana
total genus 128
structure length 366
sequence length 376
ec nomenclature ec 3.5.3.12: Agmatine deiminase.
pdb deposition date 2009-04-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04371 PAD_porph Porphyromonas-type peptidyl-arginine deiminase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.75.10.10 Alpha Beta 5-stranded Propeller L-arginine/glycine Amidinotransferase; Chain A L-arginine/glycine Amidinotransferase; Chain A 3h7kA00
9JDWA 3I2EA 2EWOA 4X8CA 3P8EA 3APMA 3BPBA 6JDWA 4YT9A 3RHYA 1WD8A 4N2FA 3P8PA 4N20A 1G61A 3B1UA 2ABRA 2CI7A 2CMUA 4E4JA 5AK8A 2AAFA 1G62A 5AK7A 2Q3UA 2CI4A 4N2DA 5AN9I 1S9RA 4N2MA 2CI3A 2ACIA 1LXYA 4N28A 3H7KA 4YTBA 3B1TA 5JDWA 4N2NA 2DEYX 4DKTA 4N22A 4X8GA 4YTGA 7JDWA 4N2CA 1WD9A 4N25A 1VKPA 2A9GA 2DEXX 4N2BA 8JDWA 2JDWA 2JERA 1WDAA 4N2EA 3H7CX 2DW5A 3I4AA 1ZBRA 4N2AA 1JDWA 4N2HA 4N24A 3JDWA 4N2GA 2CI5A 3APNA 2CI6A 4JDWA 4N2KA 2C6ZA 5M3QA 1BWDA 3HVMA 2DEWX 4N2LA 5HP5A 1JDXA 4BOFA 1RXXA 4N2IA 1XKNA 2JAJA 2JAIA 1H70A 4N26A 2CI1A 2JDXA
chains in the Genus database with same CATH superfamily
9JDWA 3I2EA 2EWOA 4X8CA 3P8EA 3APMA 3BPBA 6JDWA 4YT9A 3RHYA 1WD8A 4N2FA 3P8PA 4N20A 1G61A 3B1UA 2ABRA 1YNHA 1YNFA 2CI7A 2CMUA 4E4JA 5AK8A 2AAFA 1G62A 5AK7A 2Q3UA 2CI4A 4N2DA 5AN9I 1S9RA 4N2MA 2CI3A 2ACIA 1LXYA 4N28A 3H7KA 4YTBA 3B1TA 5JDWA 4N2NA 2DEYX 4DKTA 4N22A 1YNIA 4X8GA 4YTGA 7JDWA 4N2CA 1WD9A 4N25A 1VKPA 2A9GA 2DEXX 4N2BA 8JDWA 2JDWA 2JERA 1WDAA 4N2EA 3H7CX 2DW5A 3I4AA 1ZBRA 4N2AA 1JDWA 4N2HA 4N24A 3JDWA 4N2GA 2CI5A 3APNA 2CI6A 4JDWA 4N2KA 2C6ZA 5M3QA 1BWDA 3HVMA 2DEWX 4N2LA 5HP5A 1JDXA 4BOFA 1RXXA 4N2IA 1XKNA 2JAJA 2JAIA 1H70A 4N26A 2CI1A 2JDXA
chains in the Genus database with same CATH topology
9JDWA 3I2EA 2EWOA 4X8CA 3P8EA 3APMA 3BPBA 6JDWA 4YT9A 3RHYA 1WD8A 4N2FA 3P8PA 4N20A 1G61A 3B1UA 2ABRA 2CI7A 2CMUA 4E4JA 5AK8A 2AAFA 1G62A 5AK7A 2Q3UA 2CI4A 4N2DA 5AN9I 1S9RA 4N2MA 2CI3A 2ACIA 1LXYA 4N28A 3H7KA 4YTBA 3B1TA 5JDWA 4N2NA 2DEYX 4DKTA 4N22A 4X8GA 4YTGA 7JDWA 4N2CA 1WD9A 4N25A 1VKPA 2A9GA 2DEXX 4N2BA 8JDWA 2JDWA 2JERA 1WDAA 4N2EA 3H7CX 2DW5A 3I4AA 1ZBRA 4N2AA 1JDWA 4N2HA 4N24A 3JDWA 4N2GA 2CI5A 3APNA 2CI6A 4JDWA 4N2KA 2C6ZA 5M3QA 1BWDA 3HVMA 2DEWX 4N2LA 5HP5A 1JDXA 4BOFA 1RXXA 4N2IA 1XKNA 2JAJA 2JAIA 1H70A 4N26A 2CI1A 2JDXA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 9JDW A;  3I2E A;  2EWO A;  4X8C A;  3P8E A;  3APM A;  3BPB A;  6JDW A;  4YT9 A;  3RHY A;  1WD8 A;  4N2F A;  3P8P A;  4N20 A;  1G61 A;  3B1U A;  2ABR A;  2CI7 A;  2CMU A;  4E4J A;  5AK8 A;  2AAF A;  1G62 A;  5AK7 A;  2Q3U A;  2CI4 A;  4N2D A;  5AN9 I;  1S9R A;  4N2M A;  2CI3 A;  2ACI A;  1LXY A;  4N28 A;  3H7K A;  4YTB A;  3B1T A;  5JDW A;  4N2N A;  2DEY X;  4DKT A;  4N22 A;  4X8G A;  4YTG A;  7JDW A;  4N2C A;  1WD9 A;  4N25 A;  1VKP A;  2A9G A;  2DEX X;  4N2B A;  8JDW A;  2JDW A;  2JER A;  1WDA A;  4N2E A;  3H7C X;  2DW5 A;  3I4A A;  1ZBR A;  4N2A A;  1JDW A;  4N2H A;  4N24 A;  3JDW A;  4N2G A;  2CI5 A;  3APN A;  2CI6 A;  4JDW A;  4N2K A;  2C6Z A;  5M3Q A;  1BWD A;  3HVM A;  2DEW X;  4N2L A;  5HP5 A;  1JDX A;  4BOF A;  1RXX A;  4N2I A;  1XKN A;  2JAJ A;  2JAI A;  1H70 A;  4N26 A;  2CI1 A;  2JDX A; 
#chains in the Genus database with same CATH topology
 9JDW A;  3I2E A;  2EWO A;  4X8C A;  3P8E A;  3APM A;  3BPB A;  6JDW A;  4YT9 A;  3RHY A;  1WD8 A;  4N2F A;  3P8P A;  4N20 A;  1G61 A;  3B1U A;  2ABR A;  1YNH A;  1YNF A;  2CI7 A;  2CMU A;  4E4J A;  5AK8 A;  2AAF A;  1G62 A;  5AK7 A;  2Q3U A;  2CI4 A;  4N2D A;  5AN9 I;  1S9R A;  4N2M A;  2CI3 A;  2ACI A;  1LXY A;  4N28 A;  3H7K A;  4YTB A;  3B1T A;  5JDW A;  4N2N A;  2DEY X;  4DKT A;  4N22 A;  1YNI A;  4X8G A;  4YTG A;  7JDW A;  4N2C A;  1WD9 A;  4N25 A;  1VKP A;  2A9G A;  2DEX X;  4N2B A;  8JDW A;  2JDW A;  2JER A;  1WDA A;  4N2E A;  3H7C X;  2DW5 A;  3I4A A;  1ZBR A;  4N2A A;  1JDW A;  4N2H A;  4N24 A;  3JDW A;  4N2G A;  2CI5 A;  3APN A;  2CI6 A;  4JDW A;  4N2K A;  2C6Z A;  5M3Q A;  1BWD A;  3HVM A;  2DEW X;  4N2L A;  5HP5 A;  1JDX A;  4BOF A;  1RXX A;  4N2I A;  1XKN A;  2JAJ A;  2JAI A;  1H70 A;  4N26 A;  2CI1 A;  2JDX A; 
#chains in the Genus database with same CATH homology
 9JDW A;  3I2E A;  2EWO A;  4X8C A;  3P8E A;  3APM A;  3BPB A;  6JDW A;  4YT9 A;  3RHY A;  1WD8 A;  4N2F A;  3P8P A;  4N20 A;  1G61 A;  3B1U A;  2ABR A;  2CI7 A;  2CMU A;  4E4J A;  5AK8 A;  2AAF A;  1G62 A;  5AK7 A;  2Q3U A;  2CI4 A;  4N2D A;  5AN9 I;  1S9R A;  4N2M A;  2CI3 A;  2ACI A;  1LXY A;  4N28 A;  3H7K A;  4YTB A;  3B1T A;  5JDW A;  4N2N A;  2DEY X;  4DKT A;  4N22 A;  4X8G A;  4YTG A;  7JDW A;  4N2C A;  1WD9 A;  4N25 A;  1VKP A;  2A9G A;  2DEX X;  4N2B A;  8JDW A;  2JDW A;  2JER A;  1WDA A;  4N2E A;  3H7C X;  2DW5 A;  3I4A A;  1ZBR A;  4N2A A;  1JDW A;  4N2H A;  4N24 A;  3JDW A;  4N2G A;  2CI5 A;  3APN A;  2CI6 A;  4JDW A;  4N2K A;  2C6Z A;  5M3Q A;  1BWD A;  3HVM A;  2DEW X;  4N2L A;  5HP5 A;  1JDX A;  4BOF A;  1RXX A;  4N2I A;  1XKN A;  2JAJ A;  2JAI A;  1H70 A;  4N26 A;  2CI1 A;  2JDX 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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