1V0WA

Phospholipase d from streptomyces sp. strain pmf soaked with the substrate dibutyrylphosphatidylcholine.
Total Genus 196
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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
196
sequence length
504
structure length
496
Chain Sequence
SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAPHMNVIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANRGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICNA
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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 196
structure length 496
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 1v0wA01
3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Endonuclease Chain A 1v0wA02
1XDPA 1RH0A 1BYRA 1V0YA 1JY1A 1MU9A 3SQ7A 1V0WA 4GELA 1QZQA 1F0IA 1BYSA 3SQ5A 4H4AA 2ZE4A 4GGJA 1RG1A 4GENA 1NOPA 1V0SA 3HSIA 5BPDA 2ZE9A 4RCTA 1XDOA 2F5TX 4GEMA 1RFFA 1V0VA 1RGUA 1MU7A 5BOXA 1RG2A 2C1LA 3SQ3A 1V0RA 4URJA 1V0TA 4GGKA 3SQ8A 1V0UA 3QPHA 5LZKA 2O8RA 1RFIA 5BPIA 1RGTA 5BQTA 1Q32A
chains in the Genus database with same CATH superfamily
1XDPA 1RH0A 1BYRA 1V0YA 1JY1A 1MU9A 3SQ7A 1V0WA 1CW0A 4GELA 1QZQA 1F0IA 1BYSA 3SQ5A 4H4AA 2ZE4A 4GGJA 1RG1A 4GENA 1NOPA 1V0SA 3HSIA 5BPDA 2ZE9A 4RCTA 1XDOA 2F5TX 4GEMA 4A5ZA 1RFFA 1V0VA 1RGUA 1MU7A 5BOXA 1RG2A 2C1LA 3SQ3A 1V0RA 3R3PA 4URJA 1V0TA 4GGKA 3SQ8A 3HRLA 2YMBA 1V0UA 3QPHA 5LZKA 2O8RA 1RFIA 1VSRA 5BPIA 1ODGA 1RGTA 5BQTA 1Q32A
chains in the Genus database with same CATH topology
1XDPA 1RH0A 1BYRA 1V0YA 1JY1A 1MU9A 3SQ7A 1V0WA 4GELA 1QZQA 1F0IA 1BYSA 3SQ5A 4H4AA 2ZE4A 4GGJA 1RG1A 4GENA 1NOPA 1V0SA 3HSIA 5BPDA 2ZE9A 4RCTA 1XDOA 2F5TX 4GEMA 1RFFA 1V0VA 1RGUA 1MU7A 5BOXA 1RG2A 2C1LA 3SQ3A 1V0RA 4URJA 1V0TA 4GGKA 3SQ8A 1V0UA 3QPHA 5LZKA 2O8RA 1RFIA 5BPIA 1RGTA 5BQTA 1Q32A
chains in the Genus database with same CATH homology


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