1MH2 | pdb_00001mh2

Crystal Structure of a Zinc Containing Dimer of Phospholipase A2 from the Venom of Indian Cobra (Naja Naja Sagittifera)

• PDB DOI: https://doi.org/10.2210/pdb1MH2/pdb

• Classification: HYDROLASE
• Organism(s): Naja sagittifera
• Mutation(s): No 


• Deposited: 2002-08-19 Released: 2003-05-20 
• Deposition Author(s): Jabeen, T., Varma, A.K., Paramasivam, M., Singh, N., Singh, R.K., Sharma, S., Srinivasan, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.216 (Depositor) 
• R-Value Work: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Zinc Containing Dimer of Phospholipase A2 from the Venom of Indian cobra (Naja Naja Saggittifera)

Jabeen, T., Varma, A.K., Paramasivam, M., Singh, N., Singh, R.K., Sharma, S., Srinivasan, A., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 26.4 kDa 
• Atom Count: 2,009 
• Modeled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	A	119	Naja sagittifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P60043 (Naja sagittifera) Explore P60043  Go to UniProtKB:  P60043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	B	119	Naja sagittifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P60044 (Naja sagittifera) Explore P60044  Go to UniProtKB:  P60044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.216 (Depositor) 
• R-Value Work:  0.196 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.467	α = 90
b = 65.467	β = 90
c = 58.427	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Jabeen, T., Varma, A.K., Paramasivam, M., Singh, N., Singh, R.K., Sharma, S., Srinivasan, A., Singh, T.P.

Revision History  

• Version 1.0: 2003-05-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary