1V0YA

Phospholipase d from streptomyces sp. strain pmf soaked with the substrate dibutyrylphosphatidylcholine.
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
504
structure length
493
Chain Sequence
SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAPVIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANRGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICNA
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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 493
sequence length 504
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 1v0yA01
3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Endonuclease Chain A 1v0yA02
4H4AA 1RFIA 4GENA 4RCTA 1MU9A 4URJA 3SQ7A 1RGTA 1NOPA 1XDOA 2O8RA 4GGKA 1F0IA 5BQTA 2ZE9A 1QZQA 1RFFA 4GEMA 5BOXA 1XDPA 3SQ8A 1BYSA 4GGJA 3SQ5A 1V0WA 1RG2A 1RGUA 2F5TX 3HSIA 1V0RA 5BPDA 1V0VA 4GELA 5BPIA 1V0SA 1V0TA 5LZKA 1Q32A 1V0UA 1RH0A 3QPHA 2ZE4A 2C1LA 3SQ3A 1RG1A 1BYRA 1MU7A 1JY1A 1V0YA
chains in the Genus database with same CATH superfamily
3HRLA 4H4AA 1RFIA 2YMBA 4GENA 1MU9A 4RCTA 4URJA 3SQ7A 1RGTA 4A5ZA 1NOPA 1XDOA 2O8RA 4GGKA 1F0IA 5BQTA 2ZE9A 1QZQA 1VSRA 1RFFA 4GEMA 3R3PA 1XDPA 5BOXA 3SQ8A 1BYSA 4GGJA 3SQ5A 1V0WA 1RG2A 1RGUA 2F5TX 3HSIA 1V0RA 5BPDA 1V0VA 4GELA 1CW0A 5BPIA 1ODGA 1V0SA 1V0TA 5LZKA 1Q32A 1V0UA 1RH0A 3QPHA 2ZE4A 2C1LA 3SQ3A 1RG1A 1BYRA 1MU7A 1JY1A 1V0YA
chains in the Genus database with same CATH topology
4H4AA 1RFIA 4GENA 4RCTA 1MU9A 4URJA 3SQ7A 1RGTA 1NOPA 1XDOA 2O8RA 4GGKA 1F0IA 5BQTA 2ZE9A 1QZQA 1RFFA 4GEMA 5BOXA 1XDPA 3SQ8A 1BYSA 4GGJA 3SQ5A 1V0WA 1RG2A 1RGUA 2F5TX 3HSIA 1V0RA 5BPDA 1V0VA 4GELA 5BPIA 1V0SA 1V0TA 5LZKA 1Q32A 1V0UA 1RH0A 3QPHA 2ZE4A 2C1LA 3SQ3A 1RG1A 1BYRA 1MU7A 1JY1A 1V0YA
chains in the Genus database with same CATH homology


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