4N8S | pdb_00004n8s

Crystal Structure of the ternary complex of lipase from Thermomyces lanuginosa with Ethylacetoacetate and P-nitrobenzaldehyde at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4N8S/pdb

• Classification: HYDROLASE
• Organism(s): Thermomyces lanuginosus
• Mutation(s): No 


• Deposited: 2013-10-18 Released: 2013-11-06 
• Deposition Author(s): Kumar, M., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the ternary complex of lipase from Thermomyces lanuginosa with Ethylacetoacetate and P-nitrobenzaldehyde at 2.3 A resolution

Kumar, M., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 59.78 kDa 
• Atom Count: 4,379 
• Modeled Residue Count: 538 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B	269	Thermomyces lanuginosus	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus) Explore O59952  Go to UniProtKB:  O59952
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
XXH	D [auth A], G [auth B]	4-nitrobenzaldehyde C7 H5 N O3 BXRFQSNOROATLV-UHFFFAOYSA-N
EAC	E [auth A], H [auth B]	ethyl 3-oxobutanoate C6 H10 O3 XYIBRDXRRQCHLP-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.461	α = 90
b = 140.461	β = 90
c = 80.289	γ = 120

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: 2013-11-06 
Deposition Author(s): Kumar, M., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-16
  Changes: Structure summary