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
4HPEA 4FGIA 4HZBA 2FG0A 4FGDA 4F4MA 3A30A 3NE0A 3S0QA 3NPFA 2VPSA 3O98A 4EQAA 4F0VA 2IO9A 4JXBA 4Q4GX 3VPIA 4EQ8A 4FQBA 2K3AA 2HBWA 3M1UA 4F0WA 2LRJA 4CGKA 2K1GA 3H41A 4HZ9A 2IO8A 4OLKA 3A2ZA 4EOBA 3I86A 3PVQA 4FQAA 4Q4TA 2IO7A 3VPJA 2VOBA 4R0KA 2IOBA 2XIVA 3PBIA 3A2YA 4FGEA 4Q4NA 2EVRA 4CSHA 3GT2A 4FDYA 3KW0A 2IF6A 3PBCA 2IOAA 2VPMA 4LJ1A 4CT3A
chains in the Genus database with same CATH superfamily
4HPEA 4FGIA 4HZBA 2FG0A 4J30A 4FGDA 4F4MA 4HFKA 3A30A 3NE0A 3S0QA 3NPFA 3EBQA 2VPSA 3O98A 4HFLA 4JURA 4EQAA 4F0VA 2IO9A 4JXBA 4Q4GX 3VPIA 4EQ8A 4FQBA 2K3AA 2HBWA 3M1UA 4F0WA 2LRJA 4CGKA 2K1GA 3H41A 4HZ9A 2IO8A 4OLKA 3A2ZA 4EOBA 3I86A 3PVQA 4FQAA 4Q4TA 2IO7A 3VPJA 2WP7A 2VOBA 4R0KA 4HFFA 2IOBA 2XIVA 3PBIA 3A2YA 4FGEA 4J32A 2EVRA 4Q4NA 4CSHA 3GT2A 4FDYA 3KW0A 2IF6A 3PBCA 2IOAA 2VPMA 4LJ1A 4CT3A
chains in the Genus database with same CATH topology
4HPEA 4FGIA 4HZBA 2FG0A 4FGDA 4F4MA 3A30A 3NE0A 3S0QA 3NPFA 2VPSA 3O98A 4EQAA 4F0VA 2IO9A 4JXBA 4Q4GX 3VPIA 4EQ8A 4FQBA 2K3AA 2HBWA 3M1UA 4F0WA 2LRJA 4CGKA 2K1GA 3H41A 4HZ9A 2IO8A 4OLKA 3A2ZA 4EOBA 3I86A 3PVQA 4FQAA 4Q4TA 2IO7A 3VPJA 2VOBA 4R0KA 2IOBA 2XIVA 3PBIA 3A2YA 4FGEA 4Q4NA 2EVRA 4CSHA 3GT2A 4FDYA 3KW0A 2IF6A 3PBCA 2IOAA 2VPMA 4LJ1A 4CT3A
chains in the Genus database with same CATH homology


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