9FDE | pdb_00009fde

Lipase calB candida antarctica with lysine ligand

PDB DOI: https://doi.org/10.2210/pdb9FDE/pdb

Classification: HYDROLASE
Organism(s): Moesziomyces antarcticus
Expression System: Escherichia coli B, Escherichia coli
Mutation(s): No

Deposited: 2024-05-16 Released: 2025-05-28
Deposition Author(s): Jelsch, C., Favier, F., Didierjean, C.
Funding Organization(s): Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.257 (Depositor), 0.358 (DCC)
R-Value Work:
0.205 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Lipase calB candida antarctica with lysine ligand

Jelsch, C., Favier, F., Didierjean, C.

To be published.

Macromolecule Content

Total Structure Weight: 66.06 kDa
Atom Count: 4,803
Modeled Residue Count: 632
Deposited Residue Count: 632
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase B	A	317	Moesziomyces antarcticus	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for P41365 (Pseudozyma antarctica) Explore P41365 Go to UniProtKB: P41365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41365
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase B	B	315	Moesziomyces antarcticus	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for P41365 (Pseudozyma antarctica) Explore P41365 Go to UniProtKB: P41365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41365
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257 (Depositor), 0.358 (DCC)
R-Value Work: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.318	α = 90
b = 107.476	β = 90.043
c = 68.235	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.