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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase D LiSicTox-alphaIA1bii302Loxosceles 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / 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
PLM
Query on PLM

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J [auth A],
K [auth A],
L [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
TDA
Query on TDA

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N [auth A]N-TRIDECANOIC ACID
C13 H26 O2
SZHOJFHSIKHZHA-UHFFFAOYSA-N
DKA
Query on DKA

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I [auth A],
M [auth A]
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
OCA
Query on OCA

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G [auth A]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
SHV
Query on SHV

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H [auth A]HEPTANOIC ACID
C7 H14 O2
MNWFXJYAOYHMED-UHFFFAOYSA-N
PEG
Query on PEG

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C [auth A],
D [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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

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B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary