6XOK | pdb_00006xok

X-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6XOK/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Thermomyces lanuginosus
• Expression System: Aspergillus flavus
• Mutation(s): No 


• Deposited: 2020-07-07 Released: 2020-10-14 
• Deposition Author(s): McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.134 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.104 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.106 (Depositor) 

Starting Model: experimental

Literature

The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants

McPherson, A., Larson, S.B., Kalasky, A.

(2020) Current Enzyme Inhibition 16

• DOI: https://doi.org/10.2174/1573408016999200511090910

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.54 kDa 
• Atom Count: 2,733 
• Modeled Residue Count: 261 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	291	Thermomyces lanuginosus	Mutation(s): 0  Gene Names: LIP 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
LTV (Subject of Investigation/LOI)	J [auth A]	2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate C46 H90 O5 XHUXLZVWHLYNKB-SJARJILFSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.134 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.104 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.106 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.373	α = 90
b = 76.373	β = 90
c = 241.551	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): McPherson, A.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary