1V0WA

Phospholipase d from streptomyces sp. strain pmf soaked with the substrate dibutyrylphosphatidylcholine.
Total Genus 196
Loading diagram...

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...