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)

wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [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 F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [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]