4HMB

Crystal Structure of the complex of group II phospholipase A2 with a 3-{3-[(Dimethylamino)methyl]-1H-indol-7-yl}propan-1-ol at 2.21 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4HMB/pdb

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


• Deposited: 2012-10-18 Released: 2012-11-07 
• Deposition Author(s): Shukla, P.K., Haridas, M., Chandra, D.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Crystal Structure of the complex of group II phospholipase A2 with a 3-{3-[(Dimethylamino)methyl]-1H-indol-7-yl}propan-1-ol at 2.21 A Resolution

Shukla, P.K., Haridas, M., Chandra, D.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.86 kDa 
• Atom Count: 1,038 
• Modelled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PZZ	B [auth A]	3-{3-[(DIMETHYLAMINO)METHYL]-1H-INDOL-7-YL}PROPAN-1-OL C14 H20 N2 O KKQDXWHOFSMCSA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.077	α = 90
b = 53.077	β = 90
c = 48.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Shukla, P.K., Haridas, M., Chandra, D.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary