4YTBA

Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) in complex with dipeptide asp-gln.
Total Genus 135
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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
135
sequence length
422
structure length
422
Chain Sequence
AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNE
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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 135
structure length 422
sequence length 422
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 4ytbA01
3RHYA 4N25A 5JDWA 2ACIA 4N24A 3APNA 1G62A 1WD8A 5M3QA 2CI6A 4N22A 4YTBA 1G61A 1XKNA 4N2HA 4N28A 4E4JA 2ABRA 6JDWA 1S9RA 5AK7A 2DEXX 4N2AA 2JERA 2CI5A 1RXXA 1JDWA 4N2IA 3BPBA 2JDXA 4N2NA 4DKTA 4N2DA 1BWDA 3HVMA 3B1UA 4N26A 1VKPA 3I2EA 4N20A 2C6ZA 5AK8A 3H7CX 2DEYX 8JDWA 2CI3A 3APMA 4YTGA 4N2GA 2JAIA 1JDXA 5AN9I 4N2BA 2Q3UA 2EWOA 2JDWA 4X8CA 3P8PA 1H70A 2A9GA 4N2KA 1LXYA 2JAJA 4N2CA 2DEWX 3JDWA 4N2FA 2CMUA 7JDWA 1WDAA 2CI1A 4N2EA 2DW5A 4JDWA 4X8GA 4N2MA 4N2LA 1WD9A 9JDWA 2AAFA 2CI4A 3P8EA 1ZBRA 5HP5A 3I4AA 4BOFA 3B1TA 2CI7A 3H7KA 4YT9A
chains in the Genus database with same CATH superfamily
3RHYA 1YNFA 4N25A 5JDWA 2ACIA 4N24A 3APNA 1G62A 1WD8A 5M3QA 2CI6A 4N22A 4YTBA 1G61A 1XKNA 4N2HA 4N28A 4E4JA 2ABRA 6JDWA 1S9RA 5AK7A 2DEXX 4N2AA 2JERA 2CI5A 1RXXA 1JDWA 4N2IA 3BPBA 2JDXA 4N2NA 4DKTA 4N2DA 1BWDA 3HVMA 3B1UA 4N26A 1VKPA 3I2EA 4N20A 2C6ZA 5AK8A 3H7CX 2DEYX 8JDWA 2CI3A 3APMA 4YTGA 4N2GA 2JAIA 1JDXA 5AN9I 4N2BA 2Q3UA 2EWOA 2JDWA 1YNIA 4X8CA 3P8PA 1H70A 2A9GA 4N2KA 1LXYA 2JAJA 4N2CA 2DEWX 3JDWA 4N2FA 2CMUA 7JDWA 1WDAA 2CI1A 4N2EA 2DW5A 4JDWA 4X8GA 4N2MA 4N2LA 1WD9A 9JDWA 2AAFA 2CI4A 3P8EA 1ZBRA 5HP5A 3I4AA 4BOFA 3B1TA 2CI7A 3H7KA 1YNHA 4YT9A
chains in the Genus database with same CATH topology
3RHYA 4N25A 5JDWA 2ACIA 4N24A 3APNA 1G62A 1WD8A 5M3QA 2CI6A 4N22A 4YTBA 1G61A 1XKNA 4N2HA 4N28A 4E4JA 2ABRA 6JDWA 1S9RA 5AK7A 2DEXX 4N2AA 2JERA 2CI5A 1RXXA 1JDWA 4N2IA 3BPBA 2JDXA 4N2NA 4DKTA 4N2DA 1BWDA 3HVMA 3B1UA 4N26A 1VKPA 3I2EA 4N20A 2C6ZA 5AK8A 3H7CX 2DEYX 8JDWA 2CI3A 3APMA 4YTGA 4N2GA 2JAIA 1JDXA 5AN9I 4N2BA 2Q3UA 2EWOA 2JDWA 4X8CA 3P8PA 1H70A 2A9GA 4N2KA 1LXYA 2JAJA 4N2CA 2DEWX 3JDWA 4N2FA 2CMUA 7JDWA 1WDAA 2CI1A 4N2EA 2DW5A 4JDWA 4X8GA 4N2MA 4N2LA 1WD9A 9JDWA 2AAFA 2CI4A 3P8EA 1ZBRA 5HP5A 3I4AA 4BOFA 3B1TA 2CI7A 3H7KA 4YT9A
chains in the Genus database with same CATH homology


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