6XS3

X-ray structure of the monoclinic crystal form at 2.48 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 298 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase291Thermomyces lanuginosusMutation(s): 0 
Gene Names: LIP
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LTV (Subject of Investigation/LOI)
Query on LTV

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AA [auth E]
FA [auth D]
J [auth A]
KA [auth F]
Q [auth B]
AA [auth E],
FA [auth D],
J [auth A],
KA [auth F],
Q [auth B],
W [auth C]
2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate
C46 H90 O5
XHUXLZVWHLYNKB-SJARJILFSA-N
NAG
Query on NAG

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EA [auth D]
I [auth A]
JA [auth F]
P [auth B]
V [auth C]
EA [auth D],
I [auth A],
JA [auth F],
P [auth B],
V [auth C],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
OCA
Query on OCA

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CA [auth D]
G [auth A]
HA [auth F]
L [auth B]
S [auth C]
CA [auth D],
G [auth A],
HA [auth F],
L [auth B],
S [auth C],
X [auth E]
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
PO4
Query on PO4

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BA [auth E],
GA [auth D],
K [auth A],
M [auth B],
R [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

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DA [auth D]
H [auth A]
IA [auth F]
N [auth B]
O [auth B]
DA [auth D],
H [auth A],
IA [auth F],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.185α = 90
b = 91.366β = 94.7
c = 124.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description