PDB-10ah: Crystal structure of Danio rerio histone deacetylase 6 catalytic ...

ID or keywords:

Entry

Database: PDB / ID: 10ah

Title

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 N530D mutant complexed with trans-BAS-2

Components

Protein deacetylase HDAC6

Keywords

HYDROLASE / histone deacetylase / inhibitor / metallohydrolase

Function / homology

Function and homology information

negative regulation of cellular component organization / positive regulation of cellular component organization / tubulin deacetylase activity / mitochondrion localization / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation ...
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Goulart Stollmaier, J. / Christianson, D.W.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2026
Title: Identification of a mechanism-based binding mode for a histone deacetylase 6 inhibitor.
Authors: Rodrigues, D.A. / Wang, Y. / Goulart Stollmaier, J. / Sullivan, G.P. / D'Arcy, C. / Coughlan, A.Y. / Roe, A. / Biro, L. / Watson, P.R. / Osko, J.D. / Twamley, B. / Wynne, K. / Cagney, G. / ...

History

Deposition	Jan 8, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10ah.cif.gz	342.8 KB	Display	PDBx/mmCIF format
PDB format	pdb10ah.ent.gz		Display	PDB format
PDBx/mmJSON format	10ah.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0a/10ah ftp://data.pdbj.org/pub/pdb/validation_reports/0a/10ah	HTTPS FTP

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Related structure data

Related structure data	10aiC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein deacetylase HDAC6

B: Protein deacetylase HDAC6

hetero molecules

81.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein deacetylase HDAC6

hetero molecules

defined by author
Evidence: gel filtration
40.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein deacetylase HDAC6

hetero molecules

defined by author
40.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.766, 91.445, 96.504
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
d_1	ens_1	(chain "A" and (resid 442 through 458 or (resid 459...
d_2	ens_1	(chain "B" and (resid 442 through 474 or resid 476...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	PRO	PRO	PHE	PHE	A	A	442 - 474	8 - 40
d_1	2	ARG	ARG	ALA	ALA	A	A	476 - 690	42 - 256
d_1	3	GLU	GLU	MET	MET	A	A	692 - 754	258 - 320
d_1	4	MET	MET	LEU	LEU	A	A	756 - 797	322 - 363
d_2	1	PRO	PRO	PHE	PHE	B	B	442 - 474	8 - 40
d_2	2	ARG	ARG	ALA	ALA	B	B	476 - 690	42 - 256
d_2	3	GLU	GLU	MET	MET	B	B	692 - 754	258 - 320
d_2	4	MET	MET	LEU	LEU	B	B	756 - 797	322 - 363

NCS oper: (Code: givenMatrix: (-0.99999493401, -0.00201436365339, -0.00246460812589), (-0.00202653468909, 0.999985715839, 0.00494583405193), (0.00245461021268, 0.00495080361025, -0.9999847321)Vector: ...

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Protein , 1 types, 2 molecules AB

#1: Protein	Protein deacetylase HDAC6 / Tubulin-lysine deacetylase HDAC6 Mass: 40286.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7YT55

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Non-polymers , 5 types, 272 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-A1C4P / 1-(morpholin-4-yl)-2-sulfanylethan-1-one Mass: 161.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₁NO₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 39.92 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC6 protein, 2 mM inhibitor, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5.0, 16% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.2→42.68 Å / Num. obs: 60818 / % possible obs: 93.9 % / Redundancy: 8.6 % / B_iso Wilson estimate: 16.15 Å² / CC_1/2: 0.988 / R_merge(I) obs: 0.354 / R_pim(I) all: 0.127 / R_rim(I) all: 0.377 / Net I/σ(I): 4.6
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 8.3 % / R_merge(I) obs: 1.214 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2242 / CC_1/2: 0.832 / R_pim(I) all: 0.441 / R_rim(I) all: 1.294 / % possible all: 76.6

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS	Jan 19, 2025 (BUILT 20250714)	data reduction
Aimless	0.7.9	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→42.68 Å / SU ML: 0.2583 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2571	3786	6.24 %
R_work	0.2132	56880	-
obs	0.2159	60666	93.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 18.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→42.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5436	0	46	259	5741

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	5630
X-RAY DIFFRACTION	f_angle_d	0.891	7653
X-RAY DIFFRACTION	f_chiral_restr	0.0525	848
X-RAY DIFFRACTION	f_plane_restr	0.0091	1002
X-RAY DIFFRACTION	f_dihedral_angle_d	13.1624	2008

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.303629745802 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.23	0.306	151	0.2755	2234	X-RAY DIFFRACTION	99.54
2.23-2.26	0.3576	64	0.3001	955	X-RAY DIFFRACTION	42.8
2.26-2.29	0.3378	157	0.2753	2231	X-RAY DIFFRACTION	99.92
2.29-2.32	0.3584	142	0.2778	2247	X-RAY DIFFRACTION	99.79
2.32-2.36	0.356	171	0.2617	2258	X-RAY DIFFRACTION	99.63
2.36-2.39	0.2841	132	0.2599	2241	X-RAY DIFFRACTION	99.87
2.39-2.43	0.285	162	0.2612	2257	X-RAY DIFFRACTION	99.83
2.43-2.47	0.3435	162	0.2495	2244	X-RAY DIFFRACTION	99.92
2.47-2.52	0.2614	133	0.2499	2231	X-RAY DIFFRACTION	99.75
2.52-2.57	0.3072	142	0.2388	2274	X-RAY DIFFRACTION	99.92
2.57-2.62	0.2849	159	0.2416	2244	X-RAY DIFFRACTION	99.71
2.62-2.66	0.2905	95	0.2573	1387	X-RAY DIFFRACTION	93.92
2.68-2.74	0.2923	124	0.2444	2032	X-RAY DIFFRACTION	92.85
2.74-2.81	0.2734	167	0.2254	2211	X-RAY DIFFRACTION	99.83
2.81-2.88	0.3015	133	0.2242	2307	X-RAY DIFFRACTION	99.96
2.88-2.97	0.2757	157	0.2252	2240	X-RAY DIFFRACTION	99.88
2.97-3.06	0.2941	127	0.2127	2263	X-RAY DIFFRACTION	99.96
3.06-3.17	0.2565	161	0.2138	2232	X-RAY DIFFRACTION	99.83
3.17-3.3	0.2053	136	0.2064	2280	X-RAY DIFFRACTION	99.79
3.3-3.42	0.2167	114	0.2005	1746	X-RAY DIFFRACTION	98.73
3.46-3.63	0.255	150	0.1754	2135	X-RAY DIFFRACTION	98.75
3.63-3.86	0.2329	109	0.1811	1762	X-RAY DIFFRACTION	77.83
3.86-4.16	0.1886	134	0.1707	1916	X-RAY DIFFRACTION	85.27
4.16-4.57	0.1868	156	0.158	2241	X-RAY DIFFRACTION	99.63
4.57-5.23	0.1821	150	0.164	2239	X-RAY DIFFRACTION	99.62
5.24-6.59	0.241	158	0.2022	2240	X-RAY DIFFRACTION	99.79
6.59-42.68	0.2337	140	0.1667	2233	X-RAY DIFFRACTION	98.59

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3326109101	0.0601885126269	-0.10397821647	1.10825669738	-0.0405929639106	0.116300172182	-0.025651021372	0.165657678964	-0.0502076912662	-0.0373401961481	0.0193427015516	0.00544696450607	0.0903543649654	-0.0740695820684	0.0408883736106	0.211702740529	-0.146004107601	-0.00914994119254	0.214338764684	-0.0137692362266	0.11109862573	10.6514718534	-7.86046977056	-35.376831774
2	2.95744388245	0.93478198356	-0.483914628463	4.08390970928	-0.581419833668	3.03328929488	-0.216719619777	-0.080385172723	-0.145714896719	0.00498832635572	-0.122752316709	-0.0595839546635	0.395723306711	0.0540071392971	0.285040714121	0.234085099282	-0.115606451099	0.00106691151717	0.320822672021	0.064661178651	0.176836066137	22.4817282543	-19.9632955068	-19.9851493837
3	1.08802036535	1.10094401494	-0.685581451934	3.60821779777	-2.03184495201	1.14957965505	-0.0437002425338	-0.165099344138	-0.207107577442	0.269572822248	0.0102462581408	0.121474628843	0.0181383169304	-0.116848418521	0.03108933166	0.172368273023	-0.0623942694446	0.0594282253212	0.293215263122	0.0619502728904	0.19650205912	8.14455997399	-20.0322361028	-16.2949500268
4	0.606351423694	0.24059736315	-0.00885403436881	0.509685361774	0.0400576862776	0.401809545809	0.00922579763776	-0.0285178177968	-0.0568694739456	0.0796285224784	-0.0660054263796	-0.0177461556631	0.044030197755	-0.0633391395672	0.0607220991648	0.169432918801	-0.106780027238	-0.0112939527902	0.269624714093	0.0245625305191	0.117202992862	22.2218003504	-3.03732950766	-21.1612326343
5	1.04044906347	-0.123489328045	0.87121872931	1.27402520705	0.353820040711	1.42294353893	-0.131319951237	-0.0234818493786	0.175675418496	-0.104770574362	-0.026759133392	0.0488369251681	-0.201945607665	-0.063842074912	0.142311372722	0.242708624863	-0.123876825178	-0.0391871622151	0.229305062066	-0.00841209534544	0.10992407436	19.1072429442	12.3123475904	-17.3782777484
6	0.953074815293	0.614131034355	-0.0232521879082	0.494044023962	-0.161674488119	0.217254150876	0.017564058221	-0.0492661585169	0.121049655291	-0.0537720861497	0.00610561687778	-0.00307474812173	-0.0749542061938	-0.0102477574314	-0.0673559895623	0.171908712183	-0.141293328376	0.0190479369496	0.199317658797	0.0422316571153	0.15762594605	15.9150958537	8.47039483969	-29.4468901895
7	3.89560222883	-0.344862488044	1.03809428862	0.405533357403	0.236527466163	0.848500341594	-0.0707183278409	-0.345333855457	0.434559645412	-0.0308531068372	0.0473810362573	-0.1393946479	-0.20439066102	0.0341623214807	0.0223472880859	0.332658725774	-0.113411903491	-0.0824643130682	0.197446822679	-0.0380630932596	0.240420979463	24.191706671	16.9994279985	-12.378904868
8	0.34703225827	0.304128744158	0.127039970679	1.28906870788	0.589444981806	0.756795182422	0.00834018963969	0.017857913227	-0.0392119990593	-0.0231871568804	0.0315547695699	-0.170513715027	0.0292185570833	0.0415764970547	-0.0368365372119	0.147307816173	-0.133207199218	-0.00539915763885	0.304647861384	0.0503604773362	0.163604152261	-7.95628367577	-8.52602853357	-40.6479344543
9	0.179969438363	0.157347161401	0.00209594724471	0.135358667131	0.0104826839493	0.0441584872121	0.0276171192627	-0.0790745302021	-0.109617492344	0.0395085852807	-0.0363631774478	-0.0478397323238	0.0326960708717	-0.0246420536779	-0.0212677910335	0.171316676662	-0.150678719756	-0.00264759602564	0.169572804339	0.0146918949204	0.204917118337	-20.8650985781	-13.8377941714	-44.9057403454
10	0.32605573765	-0.0931903246504	0.0967050906472	0.534326685336	-0.06844608116	0.310651651849	-0.0761013606813	0.07445322082	-0.295245971447	-0.14032463784	0.0184507913473	-0.195715100453	0.150945078299	-0.0508340120685	0.0425997435972	0.23903222112	-0.160396833114	0.0316536317439	0.249349586654	0.00109423670636	0.23203546914	-8.16272463134	-19.9438752819	-57.1082327256
11	0.510764088986	0.170957343985	-0.109340337019	0.51787502927	-0.0887352117467	0.190623240058	-0.0219241437752	0.0519828054484	0.0287654935161	-0.0169194997975	0.0265054987156	0.0281867172137	-0.00293688757398	-0.0526813646293	-0.0128233497912	0.155970089604	-0.15413579738	0.0154804056671	0.177559272522	0.0351238951269	0.137765177042	-22.3307754842	-3.18408152127	-52.7078961611
12	1.53421637605	0.793520275254	0.860284474832	1.55129039856	0.73136421482	1.0810928136	-0.0799696070301	0.0264185695886	0.177674425028	-0.00811216466103	-0.0388255094734	0.0228630179206	-0.0710976679436	0.0302973988274	0.0699845333776	0.213631194853	-0.14550277447	-0.00969004320968	0.217743419702	-0.0353978463286	0.17995514086	-19.1352878991	12.2650237095	-56.3687356303
13	0.725149792019	0.19045362406	0.266700447182	0.389333283403	0.0289016190008	0.517911102955	-0.0466362606475	-0.0477699882298	0.134321957467	-0.0528986584315	0.0120537275722	0.0258411216362	-0.113883889563	-0.0390682204744	0.0309087398344	0.199115574663	-0.157926304914	-0.019939087641	0.223673277104	-0.00157302540889	0.131272322784	-17.4862501773	9.96315584234	-47.5261278891

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 442 through 495 )	A	A	442 - 495	1 - 54
2	2	chain 'A' and (resid 496 through 516 )	A	A	496 - 516	55 - 75
3	3	chain 'A' and (resid 517 through 537 )	A	A	517 - 537	76 - 96
4	4	chain 'A' and (resid 538 through 656 )	A	A	538 - 656	97 - 215
5	5	chain 'A' and (resid 657 through 684 )	A	A	657 - 684	216 - 243
6	6	chain 'A' and (resid 685 through 776 )	A	A	685 - 776	244 - 335
7	7	chain 'A' and (resid 777 through 797 )	A	A	777 - 797	336 - 356
8	8	chain 'B' and (resid 442 through 479 )	B	G	442 - 479	1 - 38
9	9	chain 'B' and (resid 480 through 516 )	B	G	480 - 516	39 - 75
10	10	chain 'B' and (resid 517 through 537 )	B	G	517 - 537	76 - 96
11	11	chain 'B' and (resid 538 through 656 )	B	G	538 - 656	97 - 215
12	12	chain 'B' and (resid 657 through 684 )	B	G	657 - 684	216 - 243
13	13	chain 'B' and (resid 685 through 797 )	B	G	685 - 797	244 - 356

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 272 molecules

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Experimental details

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Experiment

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Sample preparation

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 272 molecules

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 272 molecules

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