7ZW7 | pdb_00007zw7

Crystal structure of Schistosoma mansoni HDAC8 in complex with a formate molecule in the active site

PDB DOI: https://doi.org/10.2210/pdb7ZW7/pdb

Classification: HYDROLASE
Organism(s): Schistosoma mansoni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-19 Released: 2023-05-31
Deposition Author(s): Saccoccia, F., Giannaccari, M., Ruberti, G.
Funding Organization(s): Regione Lazio (Italy)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.234 (Depositor), 0.240 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Schistosoma mansoni HDAC8 in complex with a formate molecule in the active site

Saccoccia, F., Giannaccari, M., Ruberti, G.

To be published.

Macromolecule Content

Total Structure Weight: 50.21 kDa
Atom Count: 3,296
Modeled Residue Count: 408
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative histone deacetylase 1, 2,3	A	440	Schistosoma mansoni	Mutation(s): 0 EC: 3.5.1.98
UniProt
Find proteins for A0A3Q0KJ63 (Schistosoma mansoni) Explore A0A3Q0KJ63 Go to UniProtKB: A0A3Q0KJ63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3Q0KJ63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [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]
FMT (Subject of Investigation/LOI) Query on FMT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A], H [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A]
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-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]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]