8P7E

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

PDB DOI: https://doi.org/10.2210/pdb8P7E/pdb

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

Deposited: 2023-05-30 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: 1.50 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.

Macromolecule Content

Total Structure Weight: 72.26 kDa
Atom Count: 5,753
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
ABN (Subject of Investigation/LOI) Query on ABN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]