3M1UA

Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (dvu_0896) from desulfovibrio vulgaris hildenborough at 1.75 a resolution
Total Genus 114
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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
114
sequence length
430
structure length
425
Chain Sequence
SRPATPPVTPPSREGHVADLDRFPQDLRVYAMKAGADRQLLPFTEQAAQDARWNRRFFAPWRMTRISVPVKDVAAPFGTDGRPRGYAENLLPWDVTRWGALASGAALDLYPSQAWKGIVVSNSALREVPTLRPMFTAPTRAGQGYPFDMFQRTAVWMGTPVFVGHATADRAWLYVETAFAAGWMPAADVARVDDAFMTRYESGSLAAILRDDTSLNGADGTHLATAHIGTVLPLSGRTVLVPVRAPEGHAVVVPVLLTSGEAAQKPVPLTPGNMAELGNRMMGQPYGWGGLYEDRDCSSTLRDLFTPFGLWLPRNSASQAKAGRYVDIAKLDADDKEARIVAEGVPFMTLLWLRGHITLYLGLHEGQAAMFHNMWGIRTHRGGVEGRYVLGRAVVTSTRPGLDVPGNDNADGLLGRMQGMSILPG
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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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publication title Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution
rcsb
molecule tags Hydrolase
source organism Desulfovibrio vulgaris
molecule keywords Putative gamma-D-glutamyl-L-diamino acid endopeptidase
total genus 114
structure length 425
sequence length 430
chains with identical sequence B
ec nomenclature
pdb deposition date 2010-03-05

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00877 NLPC_P60 NlpC/P60 family
A PF12913 SH3_6 SH3 domain (SH3b1 type)
A PF12914 SH3_7 SH3 domain of SH3b2 type
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.1720.10 Alpha Beta Alpha-Beta Complex endopeptidase fold (from Nostoc punctiforme) endopeptidase domain like (from Nostoc punctiforme) 3m1uA01
2IOAA 2IO7A 4Q4TA 4FQAA 3PVQA 2IO8A 2K3AA 3M1UA 4FGIA 3NPFA 3A30A 2IO9A 2VPSA 4F0VA 2IOBA 4FDYA 4Q4NA 3I86A 4FGDA 2HBWA 2EVRA 2XIVA 4OLKA 4F4MA 3S0QA 4FQBA 3O98A 4EQ8A 3A2YA 3PBIA 3KW0A 3VPJA 4Q4GX 4HZ9A 4CGKA 4F0WA 3PBCA 2LRJA 4LJ1A 2VOBA 3H41A 2VPMA 2FG0A 3VPIA 3GT2A 4JXBA 4EQAA 2IF6A 2K1GA 4HZBA 4CT3A 3NE0A 4CSHA 4EOBA 4HPEA 4FGEA 4R0KA 3A2ZA
chains in the Genus database with same CATH superfamily
2IOAA 2IO7A 4Q4TA 2WP7A 4FQAA 3PVQA 2IO8A 2K3AA 3M1UA 4FGIA 3NPFA 4J30A 3A30A 2IO9A 2VPSA 4F0VA 2IOBA 4FDYA 4Q4NA 3I86A 4FGDA 2HBWA 2EVRA 2XIVA 4HFFA 4OLKA 4F4MA 3EBQA 3S0QA 4FQBA 3O98A 4EQ8A 3A2YA 3PBIA 3KW0A 4JURA 3VPJA 4Q4GX 4HFLA 4HZ9A 4CGKA 4F0WA 3PBCA 2LRJA 4LJ1A 2VOBA 3H41A 2VPMA 4J32A 2FG0A 3VPIA 3GT2A 4HFKA 4JXBA 2IF6A 2K1GA 4HZBA 4EQAA 4CT3A 3NE0A 4CSHA 4EOBA 4HPEA 4FGEA 4R0KA 3A2ZA
chains in the Genus database with same CATH topology
2IOAA 2IO7A 4Q4TA 4FQAA 3PVQA 2IO8A 2K3AA 3M1UA 4FGIA 3NPFA 3A30A 2IO9A 2VPSA 4F0VA 2IOBA 4FDYA 4Q4NA 3I86A 4FGDA 2HBWA 2EVRA 2XIVA 4OLKA 4F4MA 3S0QA 4FQBA 3O98A 4EQ8A 3A2YA 3PBIA 3KW0A 3VPJA 4Q4GX 4HZ9A 4CGKA 4F0WA 3PBCA 2LRJA 4LJ1A 2VOBA 3H41A 2VPMA 2FG0A 3VPIA 3GT2A 4JXBA 4EQAA 2IF6A 2K1GA 4HZBA 4CT3A 3NE0A 4CSHA 4EOBA 4HPEA 4FGEA 4R0KA 3A2ZA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2IOA A;  2IO7 A;  4Q4T A;  4FQA A;  3PVQ A;  2IO8 A;  2K3A A;  3M1U A;  4FGI A;  3NPF A;  3A30 A;  2IO9 A;  2VPS A;  4F0V A;  2IOB A;  4FDY A;  4Q4N A;  3I86 A;  4FGD A;  2HBW A;  2EVR A;  2XIV A;  4OLK A;  4F4M A;  3S0Q A;  4FQB A;  3O98 A;  4EQ8 A;  3A2Y A;  3PBI A;  3KW0 A;  3VPJ A;  4Q4G X;  4HZ9 A;  4CGK A;  4F0W A;  3PBC A;  2LRJ A;  4LJ1 A;  2VOB A;  3H41 A;  2VPM A;  2FG0 A;  3VPI A;  3GT2 A;  4JXB A;  4EQA A;  2IF6 A;  2K1G A;  4HZB A;  4CT3 A;  3NE0 A;  4CSH A;  4EOB A;  4HPE A;  4FGE A;  4R0K A;  3A2Z A; 
#chains in the Genus database with same CATH topology
 2IOA A;  2IO7 A;  4Q4T A;  2WP7 A;  4FQA A;  3PVQ A;  2IO8 A;  2K3A A;  3M1U A;  4FGI A;  3NPF A;  4J30 A;  3A30 A;  2IO9 A;  2VPS A;  4F0V A;  2IOB A;  4FDY A;  4Q4N A;  3I86 A;  4FGD A;  2HBW A;  2EVR A;  2XIV A;  4HFF A;  4OLK A;  4F4M A;  3EBQ A;  3S0Q A;  4FQB A;  3O98 A;  4EQ8 A;  3A2Y A;  3PBI A;  3KW0 A;  4JUR A;  3VPJ A;  4Q4G X;  4HFL A;  4HZ9 A;  4CGK A;  4F0W A;  3PBC A;  2LRJ A;  4LJ1 A;  2VOB A;  3H41 A;  2VPM A;  4J32 A;  2FG0 A;  3VPI A;  3GT2 A;  4HFK A;  4JXB A;  2IF6 A;  2K1G A;  4HZB A;  4EQA A;  4CT3 A;  3NE0 A;  4CSH A;  4EOB A;  4HPE A;  4FGE A;  4R0K A;  3A2Z A; 
#chains in the Genus database with same CATH homology
 2IOA A;  2IO7 A;  4Q4T A;  4FQA A;  3PVQ A;  2IO8 A;  2K3A A;  3M1U A;  4FGI A;  3NPF A;  3A30 A;  2IO9 A;  2VPS A;  4F0V A;  2IOB A;  4FDY A;  4Q4N A;  3I86 A;  4FGD A;  2HBW A;  2EVR A;  2XIV A;  4OLK A;  4F4M A;  3S0Q A;  4FQB A;  3O98 A;  4EQ8 A;  3A2Y A;  3PBI A;  3KW0 A;  3VPJ A;  4Q4G X;  4HZ9 A;  4CGK A;  4F0W A;  3PBC A;  2LRJ A;  4LJ1 A;  2VOB A;  3H41 A;  2VPM A;  2FG0 A;  3VPI A;  3GT2 A;  4JXB A;  4EQA A;  2IF6 A;  2K1G A;  4HZB A;  4CT3 A;  3NE0 A;  4CSH A;  4EOB A;  4HPE A;  4FGE A;  4R0K A;  3A2Z 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)

 
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