2JERA

Agmatine deiminase of enterococcus faecalis catalyzing its reaction.
Total Genus 116
50100150200250300350020406080100120
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
116
sequence length
366
structure length
365
Chain Sequence
AKRIVGSTPKQDGFRMPGEFEPQEKVWMIWPERPDNWRDGGKPVQEAFTNVAKAISQFTPMNVVVSQQQFQNCRRQLPPEITVYEMSNNDAWVRDCGPSFVINDHGEIRGVDWTFNAWGGLVDGLYFPWDQDDLVAQKICEIEHVDSYRTDDFVLEGGSFHVDGQGTVLTTEMCLLSEGRNPQLSKEAIEQKLCDYLNVEKVLWLGDGIDPEETNGHVDDVACFIAPGEVACIYTEDQNSPFYEAAQDAYQRLLKMTDAKGRQLKVHKLCCPVKNVTIKGSFKIDFVEGTMPREDGDICIASYMNFLITNDGVIVPQYGDENDRLALEQVQTMFPDKKIVGVNTVEVVYGGGNIHITQQEPKRVG
5010015020025030035035030025020015010050
020406080100Genus 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
3H1 (10-13)AH5 (187-198)S6 (148-155)EMPTYS4 (100-103)S15 (308-310)TI1 (19-22)TIV16 (354-358)S18 (359-363)AH3 (131-144)S1 (24-30)3H3 (68-70)S2 (62-66)TI2 (34-37)TII3 (288-291)3H2 (40-42)TIV2 (35-38)AH8 (346-350)TI13 (280-283)AH1 (43-58)AH2 (71-77)TI3 (79-82)TI4 (94-97)TIV3 (93-96)TIV5 (117-120)TI6 (157-160)S5 (109-115)TIV4 (104-107)TIV7 (122-125)TIV12 (212-215)TIV6 (121-124)3H4 (219-221)S8 (168-172)S7 (161-163)TIV13 (213-216)AH6 (243-255)AH4 (173-177)S9 (202-206)TI10 (211-214)TI8 (178-181)TI9 (182-185)TIV11 (209-212)TI'2 (215-218)TI14 (303-306)O1 (300-302)S11 (230-234)S10 (223-227)TIV14 (225-228)S12 (266-270)TII2 (227-230)TI11 (238-241)AH7 (323-334)S14 (298-299)TVIII2 (273-276)S13 (278-279)TII4 (295-298)S16 (313-318)TIV15 (304-307)TII'2 (310-313)TI15 (335-338)S17 (339-344)S3 (82-86)TII'1 (120-123)TIV8 (164-167)TIV1 (5-8)TI12 (259-262)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Enterococcus faecalis
publication title The Gene Cluster for Agmatine Catabolism of Enterococcus Faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing its Reaction.
pubmed doi rcsb
molecule keywords AGMATINE DEIMINASE
total genus 116
structure length 365
sequence length 366
chains with identical sequence B, C, D, E, F, G, H
ec nomenclature ec 3.5.3.12: Agmatine deiminase.
pdb deposition date 2007-01-19

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 2jerA00
4N26A 2JDWA 3B1UA 2DEXX 4X8CA 3P8PA 5AN9I 4N2DA 8JDWA 1VKPA 3HVMA 4YTGA 1WDAA 4N2LA 3RHYA 9JDWA 2AAFA 5M3QA 1G61A 2CMUA 2CI3A 4N22A 2DW5A 1JDXA 3I4AA 4E4JA 2JERA 4N2CA 2CI1A 3BPBA 3H7KA 2CI6A 2CI4A 4BOFA 7JDWA 5HP5A 3I2EA 4N2BA 1WD9A 4N20A 2ABRA 2DEYX 2EWOA 1LXYA 4JDWA 4N28A 4N2KA 4N2HA 1ZBRA 4X8GA 3APNA 2ACIA 2CI7A 4N25A 2JAJA 4N2MA 1S9RA 5JDWA 2Q3UA 3JDWA 5AK8A 4YT9A 3B1TA 4N2EA 1H70A 5AK7A 4N2NA 2CI5A 2C6ZA 4YTBA 2JDXA 4N2AA 2JAIA 4N2FA 2A9GA 3APMA 3P8EA 6JDWA 1JDWA 4N24A 4N2IA 3H7CX 1WD8A 1XKNA 1RXXA 1BWDA 4N2GA 4DKTA 2DEWX 1G62A
chains in the Genus database with same CATH superfamily
4N26A 2JDWA 3B1UA 2DEXX 4X8CA 3P8PA 5AN9I 4N2DA 8JDWA 1VKPA 3HVMA 4YTGA 1WDAA 4N2LA 3RHYA 9JDWA 2AAFA 5M3QA 1G61A 2CMUA 2CI3A 4N22A 2DW5A 1JDXA 3I4AA 4E4JA 2JERA 4N2CA 2CI1A 3BPBA 3H7KA 2CI6A 2CI4A 4BOFA 7JDWA 5HP5A 3I2EA 4N2BA 1WD9A 4N20A 2ABRA 2DEYX 2EWOA 1LXYA 4JDWA 4N28A 4N2KA 1YNIA 4N2HA 1ZBRA 4X8GA 3APNA 2ACIA 2CI7A 4N25A 2JAJA 4N2MA 1S9RA 5JDWA 2Q3UA 3JDWA 5AK8A 4YT9A 3B1TA 4N2EA 1H70A 5AK7A 4N2NA 1YNFA 2CI5A 2C6ZA 4YTBA 2JDXA 4N2AA 2JAIA 4N2FA 2A9GA 3APMA 3P8EA 6JDWA 1JDWA 4N24A 1YNHA 4N2IA 3H7CX 1WD8A 1XKNA 1RXXA 1BWDA 4N2GA 4DKTA 2DEWX 1G62A
chains in the Genus database with same CATH topology
4N26A 2JDWA 3B1UA 2DEXX 4X8CA 3P8PA 5AN9I 4N2DA 8JDWA 1VKPA 3HVMA 4YTGA 1WDAA 4N2LA 3RHYA 9JDWA 2AAFA 5M3QA 1G61A 2CMUA 2CI3A 4N22A 2DW5A 1JDXA 3I4AA 4E4JA 2JERA 4N2CA 2CI1A 3BPBA 3H7KA 2CI6A 2CI4A 4BOFA 7JDWA 5HP5A 3I2EA 4N2BA 1WD9A 4N20A 2ABRA 2DEYX 2EWOA 1LXYA 4JDWA 4N28A 4N2KA 4N2HA 1ZBRA 4X8GA 3APNA 2ACIA 2CI7A 4N25A 2JAJA 4N2MA 1S9RA 5JDWA 2Q3UA 3JDWA 5AK8A 4YT9A 3B1TA 4N2EA 1H70A 5AK7A 4N2NA 2CI5A 2C6ZA 4YTBA 2JDXA 4N2AA 2JAIA 4N2FA 2A9GA 3APMA 3P8EA 6JDWA 1JDWA 4N24A 4N2IA 3H7CX 1WD8A 1XKNA 1RXXA 1BWDA 4N2GA 4DKTA 2DEWX 1G62A
chains in the Genus database with same CATH homology


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