4YT9A

Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) substrate-unbound.
Total Genus 133
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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
133
sequence length
421
structure length
418
Chain Sequence
AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTMN
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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 Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.
pubmed doi rcsb
total genus 133
structure length 418
sequence length 421
ec nomenclature ec 3.5.3.-:
pdb deposition date 2015-03-17

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 4yt9A01
1JDWA 1WD8A 2CI5A 2JDXA 4JDWA 4N2CA 4N2EA 4N26A 2Q3UA 3I4AA 4N2DA 2EWOA 4N2FA 3JDWA 6JDWA 4X8GA 1H70A 4N2IA 4YT9A 5M3QA 2AAFA 1RXXA 4YTGA 3HVMA 9JDWA 1VKPA 3APNA 2CI6A 3RHYA 4N2MA 1G61A 4N24A 3I2EA 3H7KA 4N2KA 5AK8A 2ABRA 4N2GA 1G62A 2JDWA 1WDAA 2CI1A 4N20A 4N2AA 4N2LA 4X8CA 3P8EA 1ZBRA 5AK7A 5HP5A 2DEXX 1S9RA 3P8PA 3APMA 2JAIA 5JDWA 2DEYX 4N25A 5AN9I 4DKTA 3B1UA 2C6ZA 1WD9A 4N22A 7JDWA 2CMUA 1JDXA 2DEWX 2ACIA 3B1TA 8JDWA 1BWDA 2CI7A 2A9GA 1LXYA 4BOFA 2CI4A 2JERA 2DW5A 4N2HA 3BPBA 2JAJA 2CI3A 4YTBA 1XKNA 4N2NA 4E4JA 4N2BA 4N28A 3H7CX
chains in the Genus database with same CATH superfamily
1JDWA 1WD8A 2CI5A 2JDXA 4JDWA 4N2CA 4N2EA 4N26A 2Q3UA 3I4AA 4N2DA 2EWOA 4N2FA 3JDWA 6JDWA 4X8GA 1H70A 4N2IA 4YT9A 5M3QA 2AAFA 1RXXA 4YTGA 3HVMA 9JDWA 1VKPA 3APNA 2CI6A 3RHYA 4N2MA 1G61A 4N24A 3I2EA 3H7KA 4N2KA 5AK8A 2ABRA 4N2GA 1G62A 2JDWA 1YNIA 1WDAA 2CI1A 4N20A 4N2AA 4N2LA 1YNFA 4X8CA 3P8EA 1ZBRA 5AK7A 5HP5A 2DEXX 1S9RA 3P8PA 3APMA 2JAIA 5JDWA 2DEYX 4N25A 5AN9I 4DKTA 3B1UA 2C6ZA 1WD9A 4N22A 7JDWA 2CMUA 1JDXA 2DEWX 2ACIA 3B1TA 8JDWA 1BWDA 2CI7A 2A9GA 1YNHA 1LXYA 4BOFA 2CI4A 2JERA 2DW5A 4N2HA 3BPBA 2JAJA 2CI3A 4YTBA 1XKNA 4N2NA 4E4JA 4N2BA 4N28A 3H7CX
chains in the Genus database with same CATH topology
1JDWA 1WD8A 2CI5A 2JDXA 4JDWA 4N2CA 4N2EA 4N26A 2Q3UA 3I4AA 4N2DA 2EWOA 4N2FA 3JDWA 6JDWA 4X8GA 1H70A 4N2IA 4YT9A 5M3QA 2AAFA 1RXXA 4YTGA 3HVMA 9JDWA 1VKPA 3APNA 2CI6A 3RHYA 4N2MA 1G61A 4N24A 3I2EA 3H7KA 4N2KA 5AK8A 2ABRA 4N2GA 1G62A 2JDWA 1WDAA 2CI1A 4N20A 4N2AA 4N2LA 4X8CA 3P8EA 1ZBRA 5AK7A 5HP5A 2DEXX 1S9RA 3P8PA 3APMA 2JAIA 5JDWA 2DEYX 4N25A 5AN9I 4DKTA 3B1UA 2C6ZA 1WD9A 4N22A 7JDWA 2CMUA 1JDXA 2DEWX 2ACIA 3B1TA 8JDWA 1BWDA 2CI7A 2A9GA 1LXYA 4BOFA 2CI4A 2JERA 2DW5A 4N2HA 3BPBA 2JAJA 2CI3A 4YTBA 1XKNA 4N2NA 4E4JA 4N2BA 4N28A 3H7CX
chains in the Genus database with same CATH homology


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