9GN7

Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in Complex with the inhibitor TSA

PDB DOI: https://doi.org/10.2210/pdb9GN7/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae subsp. ozaenae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-30 Released: 2024-11-06
Deposition Author(s): Qin, C., Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.186
R-Value Work: 0.148

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

Distribution and diversity of classical deacylases in bacteria

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoeker, O., Wang, N., Hocking, D., Jebeli, L., Girbardt, B., Berndt, L., Weis, D.M., Janetzky, M., Zuehlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nature Communications

Macromolecule Content

Total Structure Weight: 42.34 kDa
Atom Count: 2,985
Modelled Residue Count: 370
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deacetylase	A	382	Klebsiella pneumoniae subsp. ozaenae	Mutation(s): 0 Gene Names: hdaH, NCTC10313_02007, NCTC5050_05964 EC: 3.5.1
UniProt
Find proteins for A0A377Z5F6 (Klebsiella pneumoniae subsp. ozaenae) Explore A0A377Z5F6 Go to UniProtKB: A0A377Z5F6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A377Z5F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TSN (Subject of Investigation/LOI) Query on TSN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRICHOSTATIN A C₁₇ H₂₂ N₂ O₃ RTKIYFITIVXBLE-QEQCGCAPSA-N		Interactions Focus chain F [auth A]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]