3CBI | pdb_00003cbi

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AJMClick on this verticalbar to view detailsBest fitted ANNClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase A2 VRV-PL-VIIIa
A, B, C, D
121Daboia russelii pulchellaMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii)
Explore P59071 
Go to UniProtKB:  P59071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59071
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJM
Query on AJM
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]		AJMALINE
C18 H22 N2 O2
CFEPCEVMXPTZPJ-OGDRVKPDSA-N
ANN
Query on ANN
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]		4-METHOXYBENZOIC ACID
C8 H8 O3
ZEYHEAKUIGZSGI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.210 (DCC) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.799α = 90
b = 108.799β = 90
c = 43.339γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AJMClick on this verticalbar to view detailsBest fitted ANNClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary