5AK8A

Structure of c351a mutant of porphyromonas gingivalis peptidylarginine deiminase
Total Genus 140
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
140
sequence length
419
structure length
419
Chain Sequence
SMNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHARTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNE
50100150200250300350400400300200100
020406080100120140Genus 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
AH4 (196-201)EMPTYTIV4 (138-141)AH1 (77-86)S14 (299-301)S5 (134-138)AH2 (96-109)TI2 (128-131)AH3 (155-168)3H1 (113-115)S4 (116-120)TIV2 (127-130)TI3 (129-132)S6 (142-150)TI5 (232-235)AH7 (313-326)TIV11 (400-403)TIV6 (187-190)3H2 (181-183)S7 (172-179)S10 (222-225)S8 (184-186)S9 (191-194)AH5 (207-218)TVIII1 (203-206)S15 (304-309)S12 (248-253)3H3 (237-239)S22 (408-411)TI4 (202-205)S11 (241-245)TIV7 (243-246)AH6 (260-273)TI6 (245-248)TII'1 (301-304)TI7 (255-258)S13 (283-288)TIV9 (295-298)S16 (331-336)TII1 (327-330)S23 (413-416)TIV12 (414-417)S24 (419-424)S20 (378-386)TII2 (416-419)TVIII3 (375-378)S19 (371-373)TI10 (338-341)TI11 (344-347)S21 (392-401)3H4 (349-352)S18 (362-366)S17 (354-357)TI12 (358-361)TI13 (386-389)TI'1 (401-404)S2 (64-70)TI1 (59-62)TVIII2 (220-223)TI8 (276-279)TIV8 (289-292)TI9 (294-297)S1 (55-57)TIV3 (137-140)O1 (152-154)S3 (88-93)TIV1 (70-73)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Porphyromonas gingivalis
publication title Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.
pubmed doi rcsb
molecule keywords PEPTIDYLARGININE DEIMINASE
total genus 140
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 5ak8A01
2CI3A 3BPBA 4BOFA 4N2HA 4N2MA 3RHYA 3P8EA 2CI7A 1VKPA 4X8CA 2Q3UA 4N24A 2DEYX 4YTBA 3H7KA 2C6ZA 1LXYA 3I2EA 2A9GA 2CMUA 5HP5A 4YT9A 2CI5A 1S9RA 4N2EA 4N2LA 2CI1A 4N2NA 2JAJA 4E4JA 2CI4A 4N2IA 2DW5A 1H70A 4N2BA 1G62A 7JDWA 2JAIA 1WD8A 2ABRA 4N2GA 2DEXX 4JDWA 5M3QA 2JDWA 8JDWA 1BWDA 2DEWX 1G61A 1ZBRA 2ACIA 5AK7A 4N25A 3P8PA 4N2DA 2CI6A 3APMA 4N22A 1WDAA 4N26A 1RXXA 3HVMA 3B1UA 1JDWA 2JDXA 6JDWA 5AN9I 3I4AA 3H7CX 4N2CA 4N2AA 4N20A 4YTGA 4DKTA 1JDXA 4N28A 5AK8A 3APNA 3B1TA 4X8GA 1XKNA 4N2KA 5JDWA 4N2FA 1WD9A 2JERA 2AAFA 9JDWA 3JDWA 2EWOA
chains in the Genus database with same CATH superfamily
2CI3A 3BPBA 4BOFA 4N2HA 4N2MA 3RHYA 3P8EA 2CI7A 1VKPA 4X8CA 2Q3UA 4N24A 2DEYX 4YTBA 3H7KA 2C6ZA 1LXYA 3I2EA 2A9GA 2CMUA 5HP5A 4YT9A 2CI5A 1S9RA 4N2EA 1YNFA 4N2LA 2CI1A 4N2NA 2JAJA 4E4JA 2CI4A 4N2IA 2DW5A 1H70A 4N2BA 1G62A 7JDWA 2JAIA 1WD8A 2ABRA 4N2GA 2DEXX 4JDWA 5M3QA 2JDWA 8JDWA 1BWDA 2DEWX 1G61A 1ZBRA 1YNHA 2ACIA 5AK7A 4N25A 3P8PA 4N2DA 2CI6A 3APMA 4N22A 1WDAA 4N26A 1RXXA 3HVMA 3B1UA 1JDWA 1YNIA 2JDXA 6JDWA 5AN9I 3I4AA 3H7CX 4N2CA 4N2AA 4N20A 4YTGA 4DKTA 1JDXA 4N28A 5AK8A 3APNA 3B1TA 4X8GA 1XKNA 4N2KA 5JDWA 4N2FA 1WD9A 2JERA 2AAFA 9JDWA 3JDWA 2EWOA
chains in the Genus database with same CATH topology
2CI3A 3BPBA 4BOFA 4N2HA 4N2MA 3RHYA 3P8EA 2CI7A 1VKPA 4X8CA 2Q3UA 4N24A 2DEYX 4YTBA 3H7KA 2C6ZA 1LXYA 3I2EA 2A9GA 2CMUA 5HP5A 4YT9A 2CI5A 1S9RA 4N2EA 4N2LA 2CI1A 4N2NA 2JAJA 4E4JA 2CI4A 4N2IA 2DW5A 1H70A 4N2BA 1G62A 7JDWA 2JAIA 1WD8A 2ABRA 4N2GA 2DEXX 4JDWA 5M3QA 2JDWA 8JDWA 1BWDA 2DEWX 1G61A 1ZBRA 2ACIA 5AK7A 4N25A 3P8PA 4N2DA 2CI6A 3APMA 4N22A 1WDAA 4N26A 1RXXA 3HVMA 3B1UA 1JDWA 2JDXA 6JDWA 5AN9I 3I4AA 3H7CX 4N2CA 4N2AA 4N20A 4YTGA 4DKTA 1JDXA 4N28A 5AK8A 3APNA 3B1TA 4X8GA 1XKNA 4N2KA 5JDWA 4N2FA 1WD9A 2JERA 2AAFA 9JDWA 3JDWA 2EWOA
chains in the Genus database with same CATH homology


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