1U4J

Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1U4J/pdb

• Classification: HYDROLASE
• Organism(s): Bungarus caeruleus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2004-07-26 Released: 2004-08-10 
• Deposition Author(s): Singh, G., Gourinath, S., Sharma, S., Bhanumathi, S., Betzel, C., Srinivasan, A., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.62 kDa 
• Atom Count: 2,033 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phospholipase A2 isoform 2	A, B	118	Bungarus caeruleus	Mutation(s): 0  EC: 3.1.1.4 Membrane Entity: Yes
UniProt
Find proteins for Q6SLM1 (Bungarus caeruleus) Explore Q6SLM1  Go to UniProtKB:  Q6SLM1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	G [auth B], H [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
ACY	E [auth A], F [auth A], K [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	D [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.36	α = 90
b = 80.36	β = 90
c = 99.44	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Singh, G., Gourinath, S., Sharma, S., Bhanumathi, S., Betzel, C., Srinivasan, A., Singh, T.P.

Revision History  

• Version 1.0: 2004-08-10
  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: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary