4S0X

Structure of three phase partition - treated lipase from Thermomyces lanuginosa in complex with lauric acid at 2.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted DAOClick on this verticalbar to view detailsBest fitted XXHClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structure of three phase partition - treated lipase from Thermomyces lanuginosa in complex with lauric acid at 2.1 A resolution

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase
A, B
269Thermomyces lanuginosusMutation(s): 0 
EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus)
Explore O59952 
Go to UniProtKB:  O59952
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59952
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
DAO
Query on DAO

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I [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
XXH
Query on XXH

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O [auth B]4-nitrobenzaldehyde
C7 H5 N O3
BXRFQSNOROATLV-UHFFFAOYSA-N
GOL
Query on GOL

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D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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M [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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H [auth A],
N [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.997α = 90
b = 139.997β = 90
c = 80.492γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted DAOClick on this verticalbar to view detailsBest fitted XXHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-10-16
    Changes: Structure summary