4YTGA

Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) mutant c351a in complex with dipeptide met-arg.
Total Genus 137
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
137
sequence length
420
structure length
417
Chain Sequence
AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHARTHEVADKGYLYIKHYPILGEQDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCM
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)AH4 (196-201)S2 (64-70)AH1 (77-85)S15 (304-309)AH2 (96-109)TI3 (129-132)3H1 (113-115)AH3 (155-168)S4 (116-120)TIV2 (127-130)S5 (134-138)TIV3 (138-141)O1 (152-154)S6 (142-150)TI6 (232-235)AH7 (313-326)TIV10 (400-403)3H2 (181-183)S9 (191-195)S7 (172-179)S8 (184-186)TIV5 (187-190)AH5 (207-218)S12 (248-253)TII'1 (301-304)TI8 (255-258)TI4 (202-205)S13 (283-288)S22 (408-411)TIV6 (243-246)TVIII1 (220-223)S10 (222-226)S11 (241-245)TI5 (228-231)TI7 (245-248)AH6 (260-273)S14 (299-301)TI9 (276-279)TIV7 (289-292)TI10 (294-297)TIV8 (295-298)S21 (392-401)S16 (331-336)TII1 (327-330)TVIII2 (414-417)S19 (371-373)TI11 (338-341)TIV9 (339-342)TI12 (344-347)3H4 (349-352)S18 (362-366)S17 (354-357)TI14 (386-389)S20 (379-386)S23 (413-416)TI'1 (401-404)S3 (88-93)TIV1 (70-73)TI1 (59-62)3H3 (237-239)TI13 (358-361)S1 (55-57)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Porphyromonas gingivalis (strain atcc baa-308 / w83)
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 137
structure length 417
sequence length 420
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 4ytgA01
4N2AA 4N2BA 4N22A 4N2IA 3I2EA 2CI3A 1LXYA 2DEYX 2CI7A 3BPBA 4N28A 1WD9A 6JDWA 4BOFA 4N26A 1WD8A 4N2KA 3HVMA 1VKPA 5AK7A 1WDAA 1JDWA 2DEWX 4N2HA 4X8CA 2CI4A 2JERA 3I4AA 3APMA 2JDXA 4N2GA 2C6ZA 2Q3UA 4N20A 3APNA 2DEXX 3B1UA 3H7CX 1H70A 1RXXA 4N24A 2JDWA 4DKTA 4N2EA 1G62A 3RHYA 4X8GA 5JDWA 2CI5A 1S9RA 2ABRA 3B1TA 4YTGA 1BWDA 8JDWA 4YTBA 4YT9A 4N2LA 3JDWA 2JAJA 2CI6A 2CMUA 2JAIA 3P8EA 2DW5A 9JDWA 2ACIA 2EWOA 1XKNA 1G61A 4N2FA 5HP5A 1ZBRA 7JDWA 3P8PA 4E4JA 5AN9I 3H7KA 4N2DA 4N2MA 4N25A 2CI1A 4JDWA 4N2NA 5M3QA 5AK8A 4N2CA 2AAFA 2A9GA 1JDXA
chains in the Genus database with same CATH superfamily
4N2AA 4N2BA 4N22A 4N2IA 3I2EA 2CI3A 1LXYA 2DEYX 1YNFA 2CI7A 3BPBA 4N28A 1WD9A 6JDWA 4BOFA 4N26A 1WD8A 4N2KA 3HVMA 1VKPA 5AK7A 1WDAA 1JDWA 2DEWX 4N2HA 4X8CA 2CI4A 2JERA 3I4AA 3APMA 2JDXA 4N2GA 2C6ZA 2Q3UA 4N20A 3APNA 2DEXX 3B1UA 3H7CX 1H70A 1RXXA 1YNIA 4N24A 2JDWA 4DKTA 4N2EA 1G62A 3RHYA 4X8GA 5JDWA 2CI5A 1S9RA 2ABRA 3B1TA 4YTGA 1BWDA 8JDWA 4YTBA 4YT9A 1YNHA 3JDWA 4N2LA 2JAJA 2CI6A 2CMUA 2JAIA 3P8EA 2DW5A 9JDWA 2ACIA 2EWOA 1XKNA 1G61A 4N2FA 5HP5A 1ZBRA 7JDWA 3P8PA 4E4JA 5AN9I 3H7KA 4N2DA 4N2MA 4N25A 2CI1A 4JDWA 4N2NA 5M3QA 5AK8A 4N2CA 2AAFA 2A9GA 1JDXA
chains in the Genus database with same CATH topology
4N2AA 4N2BA 4N22A 4N2IA 3I2EA 2CI3A 1LXYA 2DEYX 2CI7A 3BPBA 4N28A 1WD9A 6JDWA 4BOFA 4N26A 1WD8A 4N2KA 3HVMA 1VKPA 5AK7A 1WDAA 1JDWA 2DEWX 4N2HA 4X8CA 2CI4A 2JERA 3I4AA 3APMA 2JDXA 4N2GA 2C6ZA 2Q3UA 4N20A 3APNA 2DEXX 3B1UA 3H7CX 1H70A 1RXXA 4N24A 2JDWA 4DKTA 4N2EA 1G62A 3RHYA 4X8GA 5JDWA 2CI5A 1S9RA 2ABRA 3B1TA 4YTGA 1BWDA 8JDWA 4YTBA 4YT9A 4N2LA 3JDWA 2JAJA 2CI6A 2CMUA 2JAIA 3P8EA 2DW5A 9JDWA 2ACIA 2EWOA 1XKNA 1G61A 4N2FA 5HP5A 1ZBRA 7JDWA 3P8PA 4E4JA 5AN9I 3H7KA 4N2DA 4N2MA 4N25A 2CI1A 4JDWA 4N2NA 5M3QA 5AK8A 4N2CA 2AAFA 2A9GA 1JDXA
chains in the Genus database with same CATH homology


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