4RW3

Structural insights into substrate binding of brown spider venom class II phospholipases D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into Substrate Binding of Brown Spider Venom Class II Phospholipases D.

Coronado, M.A.Ullah, A.da Silva, L.S.Chaves-Moreira, D.Vuitika, L.Chaim, O.M.Veiga, S.S.Chahine, J.Murakami, M.T.Arni, R.K.

(2015) Curr Protein Pept Sci 16: 768-774

  • DOI: 10.2174/1389203716666150505231625
  • Primary Citation of Related Structures:  
    4RW3, 4RW5

  • PubMed Abstract: 
  • Phospholipases D (PLDs), the major dermonecrotic factors from brown spider venoms, trigger a range of biological reactions both in vitro and in vivo. Despite their clinical relevance in loxoscelism, structural data is restricted to the apo-form of these enzymes, which has been instrumental in understanding the functional differences between the class I and II spider PLDs ...

    Phospholipases D (PLDs), the major dermonecrotic factors from brown spider venoms, trigger a range of biological reactions both in vitro and in vivo. Despite their clinical relevance in loxoscelism, structural data is restricted to the apo-form of these enzymes, which has been instrumental in understanding the functional differences between the class I and II spider PLDs. The crystal structures of the native class II PLD from Loxosceles intermedia complexed with myo-inositol 1-phosphate and the inactive mutant H12A complexed with fatty acids indicate the existence of a strong ligand-dependent conformation change of the highly conserved aromatic residues, Tyr 223 and Trp225 indicating their roles in substrate binding. These results provided insights into the structural determinants for substrate recognition and binding by class II PLDs.


    Organizational Affiliation

    Centro Multiusuario de Inovacao Biomolecular, Departamento de Fisica, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto, 15054-000 SP, Brazil. arni@sjrp.unesp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase D LiSicTox-alphaIA1biiA302Loxosceles intermediaMutation(s): 0 
EC: 3.1.4.4 (PDB Primary Data), 4.6.1 (UniProt)
UniProt
Find proteins for P0CE82 (Loxosceles intermedia)
Explore P0CE82 
Go to UniProtKB:  P0CE82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE82
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPD
Query on IPD

Download Ideal Coordinates CCD File 
E [auth A]D-MYO-INOSITOL-1-PHOSPHATE
C6 H11 O9 P
INAPMGSXUVUWAF-UOTPTPDRSA-L
 Ligand Interaction
PLM
Query on PLM

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
TDA
Query on TDA

Download Ideal Coordinates CCD File 
N [auth A]N-TRIDECANOIC ACID
C13 H26 O2
SZHOJFHSIKHZHA-UHFFFAOYSA-N
 Ligand Interaction
DKA
Query on DKA

Download Ideal Coordinates CCD File 
I [auth A],
M [auth A]
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
OCA
Query on OCA

Download Ideal Coordinates CCD File 
G [auth A]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
SHV
Query on SHV

Download Ideal Coordinates CCD File 
H [auth A]HEPTANOIC ACID
C7 H14 O2
MNWFXJYAOYHMED-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.81α = 90
b = 49.3β = 105.83
c = 56.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references