5AK7A

Structure of wt porphyromonas gingivalis peptidylarginine deiminase
Total Genus 141
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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
141
sequence length
419
structure length
419
Chain Sequence
SMNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNE
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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 PEPTIDYLARGININE DEIMINASE
publication title Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.
pubmed doi rcsb
source organism Porphyromonas gingivalis
total genus 141
structure length 419
sequence length 419
ec nomenclature ec 3.5.3.-:
pdb deposition date 2015-03-02

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 5ak7A01
1G61A 4N20A 4YTGA 4YTBA 4X8CA 2AAFA 2CMUA 2DEWX 3I2EA 6JDWA 2CI7A 1BWDA 2JDXA 4N2BA 2JAJA 1G62A 2DEYX 1JDWA 3I4AA 4N2EA 4DKTA 8JDWA 2CI5A 5AN9I 4N22A 3P8EA 2CI4A 4X8GA 1JDXA 3RHYA 2Q3UA 3BPBA 2CI6A 3H7KA 2JDWA 1WDAA 4N2KA 5JDWA 1WD8A 3B1TA 4N2HA 5M3QA 1H70A 4N2NA 2DEXX 3P8PA 7JDWA 2ABRA 4YT9A 1VKPA 2C6ZA 4N28A 3APMA 3JDWA 2DW5A 1LXYA 4N2FA 1RXXA 3HVMA 2JERA 4N26A 3APNA 3H7CX 1S9RA 5AK7A 2EWOA 2ACIA 2CI3A 4N2GA 4N25A 4N2DA 1ZBRA 1WD9A 4N2IA 1XKNA 2A9GA 4BOFA 5AK8A 5HP5A 4JDWA 4N24A 9JDWA 4N2MA 2JAIA 2CI1A 3B1UA 4N2CA 4N2LA 4N2AA 4E4JA
chains in the Genus database with same CATH superfamily
1G61A 4N20A 4YTGA 4YTBA 4X8CA 1YNFA 2AAFA 2CMUA 2DEWX 3I2EA 6JDWA 2CI7A 1YNIA 1BWDA 2JDXA 4N2BA 2JAJA 1G62A 2DEYX 1JDWA 3I4AA 4N2EA 4DKTA 8JDWA 2CI5A 5AN9I 4N22A 3P8EA 2CI4A 4X8GA 1JDXA 3RHYA 2Q3UA 3BPBA 2CI6A 3H7KA 2JDWA 1WDAA 4N2KA 5JDWA 1WD8A 3B1TA 4N2HA 5M3QA 1H70A 4N2NA 2DEXX 3P8PA 7JDWA 2ABRA 4YT9A 1VKPA 2C6ZA 4N28A 3APMA 3JDWA 2DW5A 1LXYA 4N2FA 1RXXA 3HVMA 2JERA 4N26A 3APNA 3H7CX 1S9RA 5AK7A 2EWOA 2ACIA 2CI3A 4N2GA 4N25A 4N2DA 1ZBRA 1WD9A 4N2IA 1XKNA 2A9GA 1YNHA 4BOFA 5AK8A 5HP5A 4JDWA 4N24A 9JDWA 4N2MA 2JAIA 2CI1A 3B1UA 4N2CA 4N2LA 4N2AA 4E4JA
chains in the Genus database with same CATH topology
1G61A 4N20A 4YTGA 4YTBA 4X8CA 2AAFA 2CMUA 2DEWX 3I2EA 6JDWA 2CI7A 1BWDA 2JDXA 4N2BA 2JAJA 1G62A 2DEYX 1JDWA 3I4AA 4N2EA 4DKTA 8JDWA 2CI5A 5AN9I 4N22A 3P8EA 2CI4A 4X8GA 1JDXA 3RHYA 2Q3UA 3BPBA 2CI6A 3H7KA 2JDWA 1WDAA 4N2KA 5JDWA 1WD8A 3B1TA 4N2HA 5M3QA 1H70A 4N2NA 2DEXX 3P8PA 7JDWA 2ABRA 4YT9A 1VKPA 2C6ZA 4N28A 3APMA 3JDWA 2DW5A 1LXYA 4N2FA 1RXXA 3HVMA 2JERA 4N26A 3APNA 3H7CX 1S9RA 5AK7A 2EWOA 2ACIA 2CI3A 4N2GA 4N25A 4N2DA 1ZBRA 1WD9A 4N2IA 1XKNA 2A9GA 4BOFA 5AK8A 5HP5A 4JDWA 4N24A 9JDWA 4N2MA 2JAIA 2CI1A 3B1UA 4N2CA 4N2LA 4N2AA 4E4JA
chains in the Genus database with same CATH homology


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