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.

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


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