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


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