8P7E

Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with benzylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.138 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Amide formation of (hetero)aromatic esters and primary amines in buffer catalyzed by serine hydrolases: An Asp next to Ser of the catalytic triad of serine hydrolases is crucial for activity

Zukic, E.Mokos, D.Daniel, B.Weber, M.Stix, N.Ditrich, K.Willrodt, C.Gruber, K.Kroutil, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase
A, B
329Sphingomonas sp.Mutation(s): 0 
Gene Names: LH19_08550
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ABN (Subject of Investigation/LOI)
Query on ABN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
BENZYLAMINE
C7 H9 N
WGQKYBSKWIADBV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.97α = 90
b = 88.552β = 96.17
c = 65.761γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--
Austrian Research Promotion AgencyAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release