6XRV | pdb_00006xrv

X-ray structure of the monoclinic crystal form at 1.43 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 173 K

• PDB DOI: https://doi.org/10.2210/pdb6XRV/pdb

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


• Deposited: 2020-07-13 Released: 2020-10-14 
• Deposition Author(s): McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.151 (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: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 198.65 kDa 
• Atom Count: 14,720 
• Modeled Residue Count: 1,614 
• Deposited Residue Count: 1,746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D [auth E], E [auth D], F	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LTV (Subject of Investigation/LOI)	FA [auth D], I [auth A], LA [auth F], Q [auth B], V [auth C], Z [auth E]	2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate C46 H90 O5 XHUXLZVWHLYNKB-SJARJILFSA-N
NAG	EA [auth D], H [auth A], KA [auth F], P [auth B], U [auth C], Y [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
OCA	CA [auth D], G [auth A], IA [auth F], L [auth B], S [auth C], W [auth E]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N
PO4	AA [auth E], BA [auth E], GA [auth D], HA [auth D], J [auth A], K [auth A], M [auth B], MA [auth F], R [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	DA [auth D], JA [auth F], N [auth B], O [auth B], T [auth C], X [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.929	α = 90
b = 89.937	β = 94.49
c = 123.422	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
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: Data collection, Database references, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary