8P8F

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

PDB DOI: https://doi.org/10.2210/pdb8P8F/pdb

Classification: HYDROLASE
Organism(s): Sphingomonas sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-01 Released: 2024-06-12
Deposition Author(s): Mokos, D., Gruber, K., Daniel, B.
Funding Organization(s): Austrian Science Fund, Austrian Research Promotion Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228
R-Value Work: 0.189

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.

Macromolecule Content

Total Structure Weight: 71.4 kDa
Atom Count: 5,256
Modelled Residue Count: 618
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B	329	Sphingomonas sp.	Mutation(s): 0 Gene Names: LH19_08550
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XBW (Subject of Investigation/LOI) Query on XBW Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	~{N}-(phenylmethyl)pyridine-2-carboxamide C₁₃ H₁₂ N₂ O NNIFYECULHSHBH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228
R-Value Work: 0.189
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.833	α = 90
b = 60.833	β = 90
c = 217.692	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--
Austrian Research Promotion Agency	Austria	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.