1V0VA

Phospholipase d from streptomyces sp. strain pmf soaked with the substrate dibutyrylphosphatidylcholine.
Total Genus 195
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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
195
sequence length
503
structure length
492
Chain Sequence
SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAPVIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANRGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICN
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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.

molecule tags Hydrolase
molecule keywords PHOSPHOLIPASE D
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
total genus 195
structure length 492
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 1v0vA01
3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Endonuclease Chain A 1v0vA02
1MU7A 1XDPA 3QPHA 1JY1A 4RCTA 1V0TA 1QZQA 5BPIA 2C1LA 4GGJA 1BYSA 4GEMA 1Q32A 3HSIA 1F0IA 2F5TX 5LZKA 4GGKA 2ZE4A 2O8RA 1RFIA 1V0VA 1BYRA 1V0SA 1RGTA 1XDOA 1RG1A 4GENA 2ZE9A 1RH0A 3SQ8A 5BPDA 1V0WA 1V0YA 1MU9A 4URJA 4H4AA 3SQ5A 1RG2A 1RGUA 3SQ7A 3SQ3A 4GELA 1V0UA 1NOPA 5BOXA 5BQTA 1RFFA 1V0RA
chains in the Genus database with same CATH superfamily
1MU7A 1XDPA 3QPHA 1JY1A 4RCTA 1V0TA 1QZQA 5BPIA 2C1LA 4GGJA 1BYSA 4GEMA 1Q32A 3HSIA 4A5ZA 2YMBA 1F0IA 2F5TX 1ODGA 5LZKA 4GGKA 2ZE4A 2O8RA 1RFIA 1V0VA 1BYRA 1V0SA 3R3PA 1RGTA 1XDOA 1CW0A 1RG1A 4GENA 2ZE9A 1RH0A 3SQ8A 5BPDA 1V0WA 1V0YA 1MU9A 4URJA 4H4AA 3SQ5A 1RG2A 1RGUA 3SQ7A 3HRLA 3SQ3A 4GELA 1V0UA 1NOPA 5BOXA 1VSRA 5BQTA 1RFFA 1V0RA
chains in the Genus database with same CATH topology
1MU7A 1XDPA 3QPHA 1JY1A 4RCTA 1V0TA 1QZQA 5BPIA 2C1LA 4GGJA 1BYSA 4GEMA 1Q32A 3HSIA 1F0IA 2F5TX 5LZKA 4GGKA 2ZE4A 2O8RA 1RFIA 1V0VA 1BYRA 1V0SA 1RGTA 1XDOA 1RG1A 4GENA 2ZE9A 1RH0A 3SQ8A 5BPDA 1V0WA 1V0YA 1MU9A 4URJA 4H4AA 3SQ5A 1RG2A 1RGUA 3SQ7A 3SQ3A 4GELA 1V0UA 1NOPA 5BOXA 5BQTA 1RFFA 1V0RA
chains in the Genus database with same CATH homology


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