1TDV

Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution

• PDB DOI: https://doi.org/10.2210/pdb1TDV/pdb

• Classification: HYDROLASE
• Organism(s): Daboia russelii pulchella
• Mutation(s): No 


• Deposited: 2004-05-24 Released: 2004-06-08 
• Deposition Author(s): Singh, N., Jabeen, T., Ethayathulla, A.S., Somvanshi, R.K., Sharma, S., Dey, S., Perbandt, M., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution

Singh, N., Jabeen, T., Ethayathulla, A.S., Somvanshi, R.K., Sharma, S., Dey, S., Perbandt, M., Betzel, C., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.86 kDa 
• Atom Count: 1,167 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A	121	Daboia russelii pulchella	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii) Explore P59071  Go to UniProtKB:  P59071

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YWAAAA	B	6	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.29	α = 90
b = 52.29	β = 90
c = 47.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Singh, N., Jabeen, T., Ethayathulla, A.S., Somvanshi, R.K., Sharma, S., Dey, S., Perbandt, M., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary