1V0T | Genus

Total Genus 193

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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	193
sequence length	503
structure length	491
Chain Sequence	SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAVIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANRGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICN

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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

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

publication title	The Reaction Mechanism of Phospholipase D from Streptomyces Sp. Strain Pmf. Snapshots Along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product pubmed doi rcsb
molecule keywords	PHOSPHOLIPASE D
molecule tags	Hydrolase
total genus	193
structure length	491
sequence length	503
ec nomenclature	ec 3.1.4.4: Phospholipase D.
pdb deposition date	2004-04-02

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF13091	PLDc_2	PLD-like domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Endonuclease Chain A	1v0tA01
3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Endonuclease Chain A	1v0tA02

4URJA 1V0WA 1V0YA 1V0TA 4GENA 1RG1A 1QZQA 1BYRA 1RG2A 3SQ7A 1RH0A 4RCTA 2ZE9A 1V0VA 2F5TX 1MU7A 4GGKA 4GEMA 5BPDA 1MU9A 1V0RA 5BQTA 2ZE4A 2C1LA 5BOXA 4H4AA 3QPHA 4GELA 2O8RA 1V0SA 3SQ8A 1JY1A 1RFIA 1XDOA 1RGUA 1RFFA 5BPIA 1BYSA 4GGJA 1RGTA 5LZKA 1Q32A 1F0IA 3HSIA 1V0UA 3SQ3A 1XDPA 3SQ5A 1NOPA
chains in the Genus database with same CATH superfamily

4URJA 1V0WA 1V0YA 1V0TA 2YMBA 4GENA 1QZQA 1RG1A 1VSRA 1BYRA 1RG2A 3R3PA 3SQ7A 1RH0A 4RCTA 2ZE9A 1ODGA 1V0VA 2F5TX 1MU7A 4GGKA 1CW0A 4GEMA 5BPDA 1MU9A 1V0RA 5BQTA 2ZE4A 2C1LA 5BOXA 4H4AA 3QPHA 4GELA 2O8RA 1V0SA 3SQ8A 1JY1A 1RFIA 1XDOA 1RGUA 1RFFA 5BPIA 1BYSA 4GGJA 1RGTA 5LZKA 1Q32A 1F0IA 3HSIA 1V0UA 3HRLA 4A5ZA 3SQ3A 1XDPA 3SQ5A 1NOPA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4URJ A;  1V0W A;  1V0Y A;  1V0T A;  4GEN A;  1RG1 A;  1QZQ A;  1BYR A;  1RG2 A;  3SQ7 A;  1RH0 A;  4RCT A;  2ZE9 A;  1V0V A;  2F5T X;  1MU7 A;  4GGK A;  4GEM A;  5BPD A;  1MU9 A;  1V0R A;  5BQT A;  2ZE4 A;  2C1L A;  5BOX A;  4H4A A;  3QPH A;  4GEL A;  2O8R A;  1V0S A;  3SQ8 A;  1JY1 A;  1RFI A;  1XDO A;  1RGU A;  1RFF A;  5BPI A;  1BYS A;  4GGJ A;  1RGT A;  5LZK A;  1Q32 A;  1F0I A;  3HSI A;  1V0U A;  3SQ3 A;  1XDP A;  3SQ5 A;  1NOP A; 
#chains in the Genus database with same CATH topology
 4URJ A;  1V0W A;  1V0Y A;  1V0T A;  2YMB A;  4GEN A;  1QZQ A;  1RG1 A;  1VSR A;  1BYR A;  1RG2 A;  3R3P A;  3SQ7 A;  1RH0 A;  4RCT A;  2ZE9 A;  1ODG A;  1V0V A;  2F5T X;  1MU7 A;  4GGK A;  1CW0 A;  4GEM A;  5BPD A;  1MU9 A;  1V0R A;  5BQT A;  2ZE4 A;  2C1L A;  5BOX A;  4H4A A;  3QPH A;  4GEL A;  2O8R A;  1V0S A;  3SQ8 A;  1JY1 A;  1RFI A;  1XDO A;  1RGU A;  1RFF A;  5BPI A;  1BYS A;  4GGJ A;  1RGT A;  5LZK A;  1Q32 A;  1F0I A;  3HSI A;  1V0U A;  3HRL A;  4A5Z A;  3SQ3 A;  1XDP A;  3SQ5 A;  1NOP A; 
#chains in the Genus database with same CATH homology
 4URJ A;  1V0W A;  1V0Y A;  1V0T A;  4GEN A;  1RG1 A;  1QZQ A;  1BYR A;  1RG2 A;  3SQ7 A;  1RH0 A;  4RCT A;  2ZE9 A;  1V0V A;  2F5T X;  1MU7 A;  4GGK A;  4GEM A;  5BPD A;  1MU9 A;  1V0R A;  5BQT A;  2ZE4 A;  2C1L A;  5BOX A;  4H4A A;  3QPH A;  4GEL A;  2O8R A;  1V0S A;  3SQ8 A;  1JY1 A;  1RFI A;  1XDO A;  1RGU A;  1RFF A;  5BPI A;  1BYS A;  4GGJ A;  1RGT A;  5LZK A;  1Q32 A;  1F0I A;  3HSI A;  1V0U A;  3SQ3 A;  1XDP A;  3SQ5 A;  1NOP 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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#similar chains, but unknotted
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1V0TA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations