4YTBA

Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) in complex with dipeptide asp-gln.
Total Genus 135
50100150200250300350400020406080100120140
Genus TraceResidueGenus

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
50100150200250300350400400300200100
020406080100120Genus Matrix

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
EMPTYTI2 (128-131)TI'1 (401-404)S2 (64-70)AH1 (77-85)S15 (304-309)AH2 (96-109)TI11 (344-347)TI3 (129-132)3H1 (113-115)AH3 (155-168)TIV2 (127-130)S7 (172-179)S5 (134-138)O1 (152-154)TIV3 (138-141)S9 (191-194)S6 (142-150)TI5 (232-235)AH7 (313-326)3H2 (181-183)S8 (184-186)TIV5 (187-190)AH4 (196-201)AH5 (207-218)TI7 (255-258)TI4 (202-205)S13 (283-288)S23 (413-416)TIV6 (243-246)S12 (248-253)TVIII1 (220-223)S10 (222-225)S11 (241-245)3H3 (237-239)TI6 (245-248)TI8 (276-279)S14 (299-301)TIV7 (289-292)TI9 (294-297)TIV8 (295-298)TIV10 (400-403)TIV9 (339-342)TII1 (327-330)S24 (419-424)S16 (331-336)S20 (378-386)S19 (371-373)S17 (354-357)S21 (392-401)TI12 (358-361)TI13 (386-389)TII2 (416-419)TIV11 (414-417)S22 (408-411)S3 (88-93)TI1 (59-62)S4 (116-120)AH6 (260-273)TI10 (338-341)3H4 (349-351)S18 (362-366)TVIII2 (375-378)S1 (55-57)TIV1 (70-73)Updating...
connected with : NaN
molecule tags Hydrolase
publication title Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.
pubmed doi rcsb
molecule keywords Peptidylarginine deiminase
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
5JDWA 4N20A 4BOFA 2DEWX 4N2FA 3APNA 1JDWA 5AK7A 4N2BA 4DKTA 5AN9I 3BPBA 4N2EA 5HP5A 4N2NA 7JDWA 1G61A 3H7KA 3H7CX 3B1TA 2CI5A 1XKNA 1G62A 2Q3UA 4N2IA 4N26A 4JDWA 1BWDA 2AAFA 2JDXA 4N2LA 4N2GA 1VKPA 4N28A 4YT9A 2C6ZA 2CI3A 2JAJA 4N2KA 2CMUA 3APMA 1JDXA 2ABRA 4N2MA 2A9GA 4N2CA 5M3QA 3P8PA 2ACIA 4YTGA 1LXYA 3RHYA 3I2EA 4N25A 3I4AA 4E4JA 4X8CA 4X8GA 1WD9A 2DEYX 2DEXX 4N24A 4N2DA 2DW5A 3P8EA 2CI1A 1ZBRA 3JDWA 1S9RA 9JDWA 4N2HA 1RXXA 4N2AA 4YTBA 2JDWA 1WD8A 2CI7A 2EWOA 1H70A 6JDWA 3B1UA 2JERA 2CI6A 4N22A 1WDAA 8JDWA 5AK8A 2JAIA 2CI4A 3HVMA
chains in the Genus database with same CATH superfamily
5JDWA 4N20A 4BOFA 2DEWX 4N2FA 3APNA 1JDWA 5AK7A 4N2BA 4DKTA 5AN9I 3BPBA 4N2EA 5HP5A 4N2NA 7JDWA 1G61A 3H7KA 3H7CX 3B1TA 2CI5A 1YNFA 1XKNA 1G62A 2Q3UA 4N2IA 4N26A 4JDWA 1BWDA 2AAFA 2JDXA 4N2LA 4N2GA 1VKPA 1YNIA 4N28A 4YT9A 2C6ZA 2CI3A 2JAJA 4N2KA 1YNHA 2CMUA 3APMA 1JDXA 2ABRA 4N2MA 2A9GA 4N2CA 5M3QA 3P8PA 2ACIA 4YTGA 1LXYA 3RHYA 3I2EA 4N25A 3I4AA 4E4JA 4X8CA 4X8GA 1WD9A 2DEYX 2DEXX 4N24A 4N2DA 2DW5A 3P8EA 2CI1A 1ZBRA 3JDWA 1S9RA 9JDWA 4N2HA 1RXXA 4N2AA 4YTBA 2JDWA 1WD8A 2CI7A 2EWOA 1H70A 6JDWA 3B1UA 2JERA 2CI6A 4N22A 1WDAA 8JDWA 5AK8A 2JAIA 2CI4A 3HVMA
chains in the Genus database with same CATH topology
5JDWA 4N20A 4BOFA 2DEWX 4N2FA 3APNA 1JDWA 5AK7A 4N2BA 4DKTA 5AN9I 3BPBA 4N2EA 5HP5A 4N2NA 7JDWA 1G61A 3H7KA 3H7CX 3B1TA 2CI5A 1XKNA 1G62A 2Q3UA 4N2IA 4N26A 4JDWA 1BWDA 2AAFA 2JDXA 4N2LA 4N2GA 1VKPA 4N28A 4YT9A 2C6ZA 2CI3A 2JAJA 4N2KA 2CMUA 3APMA 1JDXA 2ABRA 4N2MA 2A9GA 4N2CA 5M3QA 3P8PA 2ACIA 4YTGA 1LXYA 3RHYA 3I2EA 4N25A 3I4AA 4E4JA 4X8CA 4X8GA 1WD9A 2DEYX 2DEXX 4N24A 4N2DA 2DW5A 3P8EA 2CI1A 1ZBRA 3JDWA 1S9RA 9JDWA 4N2HA 1RXXA 4N2AA 4YTBA 2JDWA 1WD8A 2CI7A 2EWOA 1H70A 6JDWA 3B1UA 2JERA 2CI6A 4N22A 1WDAA 8JDWA 5AK8A 2JAIA 2CI4A 3HVMA
chains in the Genus database with same CATH homology


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