1V0TA

Phospholipase d from streptomyces sp. strain pmf soaked with the product glycerophosphate
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

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

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


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