9GZ5 | pdb_00009gz5

X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.

PDB DOI: https://doi.org/10.2210/pdb9GZ5/pdb

Classification: HYDROLASE
Organism(s): Leptospira interrogans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-03 Released: 2025-10-15
Deposition Author(s): Novakova, Z., Barinka, C., Motlova, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.

Novakova, Z., Barinka, C., Motlova, L.

To be published.

Macromolecule Content

Total Structure Weight: 35.68 kDa
Atom Count: 2,705
Modeled Residue Count: 300
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase	A	305	Leptospira interrogans	Mutation(s): 0 Gene Names: acuC, LA_2923
UniProt
Find proteins for Q8F254 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8F254 Go to UniProtKB: Q8F254
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8F254
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IRB (Subject of Investigation/LOI) Query on A1IRB Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	cis-5-dodecenoic acid C₁₂ H₂₂ O₂ IJBFSOLHRKELLR-BQYQJAHWSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.201 (Depositor), 0.201 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.265	α = 90
b = 61.744	β = 99.86
c = 49.481	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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.