2Q3UA

Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana at5g08170, agmatine iminohydrolase
Total Genus 111
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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
111
sequence length
372
structure length
365
Chain Sequence
RESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT
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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 Ensemble refinement of protein crystal structures: validation and application.
pubmed doi rcsb
source organism Arabidopsis thaliana
total genus 111
structure length 365
sequence length 372
chains with identical sequence B
ec nomenclature ec 3.5.3.12: Agmatine deiminase.
pdb deposition date 2007-05-30

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 2q3uA00
2Q3UA 4N2LA 4N2BA 4DKTA 4N2DA 4N26A 2CI5A 2DEYX 1JDWA 4X8CA 2C6ZA 2ABRA 1H70A 3RHYA 7JDWA 2CI1A 9JDWA 2CI4A 5HP5A 2DEWX 4N22A 4N2EA 4N24A 2DEXX 2A9GA 6JDWA 2CI7A 3BPBA 5JDWA 3I2EA 3P8EA 2EWOA 4N2KA 4BOFA 2DW5A 3JDWA 5M3QA 4N2GA 2CI6A 1WDAA 4N2HA 4JDWA 1XKNA 1S9RA 4E4JA 2AAFA 1ZBRA 1VKPA 5AK8A 3B1TA 1LXYA 3APNA 5AK7A 4N2MA 2JERA 1JDXA 2ACIA 2CI3A 2JDWA 8JDWA 4YTGA 1G61A 2JAIA 3H7CX 4N25A 4YT9A 2JDXA 4YTBA 5AN9I 1G62A 4N28A 4N20A 4N2FA 3P8PA 4N2IA 3APMA 4X8GA 3H7KA 2CMUA 1WD8A 4N2NA 4N2CA 4N2AA 3B1UA 2JAJA 1WD9A 1BWDA 1RXXA 3I4AA 3HVMA
chains in the Genus database with same CATH superfamily
2Q3UA 4N2LA 4N2BA 4DKTA 4N2DA 4N26A 2CI5A 2DEYX 1JDWA 4X8CA 2C6ZA 2ABRA 1H70A 3RHYA 7JDWA 2CI1A 9JDWA 2CI4A 5HP5A 2DEWX 1YNIA 4N22A 4N2EA 4N24A 2DEXX 2A9GA 6JDWA 2CI7A 3BPBA 5JDWA 3I2EA 3P8EA 2EWOA 4N2KA 1YNFA 4BOFA 2DW5A 3JDWA 5M3QA 4N2GA 2CI6A 1WDAA 4N2HA 4JDWA 1XKNA 1S9RA 4E4JA 2AAFA 1ZBRA 1VKPA 5AK8A 3B1TA 1LXYA 1YNHA 3APNA 5AK7A 4N2MA 2JERA 1JDXA 2ACIA 2CI3A 2JDWA 8JDWA 4YTGA 1G61A 2JAIA 3H7CX 4N25A 4YT9A 2JDXA 4YTBA 5AN9I 1G62A 4N28A 4N20A 4N2FA 3P8PA 4N2IA 3APMA 4X8GA 3H7KA 2CMUA 1WD8A 4N2NA 4N2CA 4N2AA 3B1UA 2JAJA 1WD9A 1BWDA 1RXXA 3I4AA 3HVMA
chains in the Genus database with same CATH topology
2Q3UA 4N2LA 4N2BA 4DKTA 4N2DA 4N26A 2CI5A 2DEYX 1JDWA 4X8CA 2C6ZA 2ABRA 1H70A 3RHYA 7JDWA 2CI1A 9JDWA 2CI4A 5HP5A 2DEWX 4N22A 4N2EA 4N24A 2DEXX 2A9GA 6JDWA 2CI7A 3BPBA 5JDWA 3I2EA 3P8EA 2EWOA 4N2KA 4BOFA 2DW5A 3JDWA 5M3QA 4N2GA 2CI6A 1WDAA 4N2HA 4JDWA 1XKNA 1S9RA 4E4JA 2AAFA 1ZBRA 1VKPA 5AK8A 3B1TA 1LXYA 3APNA 5AK7A 4N2MA 2JERA 1JDXA 2ACIA 2CI3A 2JDWA 8JDWA 4YTGA 1G61A 2JAIA 3H7CX 4N25A 4YT9A 2JDXA 4YTBA 5AN9I 1G62A 4N28A 4N20A 4N2FA 3P8PA 4N2IA 3APMA 4X8GA 3H7KA 2CMUA 1WD8A 4N2NA 4N2CA 4N2AA 3B1UA 2JAJA 1WD9A 1BWDA 1RXXA 3I4AA 3HVMA
chains in the Genus database with same CATH homology


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