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

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Basic information

Entry
Database: PDB / ID: 10ai
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 N530D mutant complexed with cis-BAS-2
ComponentsProtein deacetylase HDAC6
KeywordsHYDROLASE / 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 ...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 / swimming behavior / transferase activity / chromatin organization / actin binding / angiogenesis / perikaryon / axon / centrosome / dendrite / zinc ion binding / nucleus
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / : / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGoulart Stollmaier, J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: 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. / ...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. / Buglyo, P. / Liu, Y. / Griffith, D.M. / Christianson, D.W. / Chonghaile, T.N.
History
DepositionJan 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein deacetylase HDAC6
B: Protein deacetylase HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,30712
Polymers80,5732
Non-polymers73410
Water6,918384
1
A: Protein deacetylase HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7157
Polymers40,2861
Non-polymers4296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein deacetylase HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5915
Polymers40,2861
Non-polymers3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.887, 91.654, 96.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 442 through 450 or resid 452 through 690 or resid 692 through 797))
d_2ens_1(chain "B" and (resid 442 through 450 or resid 452...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROGLNGLNAA442 - 4508 - 16
d_12METMETALAALAAA452 - 69018 - 256
d_13GLUGLULEULEUAA692 - 797258 - 363
d_21PROPROGLNGLNBB442 - 4508 - 16
d_22METMETALAALABB452 - 69018 - 256
d_23GLUGLULEULEUBB692 - 797258 - 363

NCS oper: (Code: givenMatrix: (-0.999992048658, 0.00374781020919, -0.00136254857337), (0.00376669888607, 0.999892999924, -0.0141350869449), (0.00130942715741, -0.0141401068622, -0.999899166306)Vector: ...NCS oper: (Code: given
Matrix: (-0.999992048658, 0.00374781020919, -0.00136254857337), (0.00376669888607, 0.999892999924, -0.0141350869449), (0.00130942715741, -0.0141401068622, -0.999899166306)
Vector: -74.8176471257, 0.167371417958, -22.5546486692)

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Components

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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 / Mutation: N378D
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, 394 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / 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.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 protein, 2 mM inhibitor, 0.04 M Citric acid, 0.06 M BIS-TRIS propane pH 6.4, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→42.7 Å / Num. obs: 74093 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.3 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.135 / Rrim(I) all: 0.311 / Net I/σ(I): 4.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3187 / CC1/2: 0.754 / Rpim(I) all: 0.517 / Rrim(I) all: 1.204 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSJan 19, 2025 (BUILT 20250714)data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.7 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 3777 5.11 %
Rwork0.2031 70124 -
obs0.2047 73901 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 34 384 5903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695671
X-RAY DIFFRACTIONf_angle_d0.86017705
X-RAY DIFFRACTIONf_chiral_restr0.0529846
X-RAY DIFFRACTIONf_plane_restr0.00871008
X-RAY DIFFRACTIONf_dihedral_angle_d13.71522035
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.506072778043 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.31121420.29232602X-RAY DIFFRACTION98.28
2.13-2.150.32461520.29332584X-RAY DIFFRACTION98.28
2.15-2.180.32411340.27352604X-RAY DIFFRACTION98.6
2.18-2.220.32461410.26692563X-RAY DIFFRACTION98.72
2.22-2.250.31851370.25662617X-RAY DIFFRACTION98.67
2.25-2.280.30071240.25962607X-RAY DIFFRACTION99.02
2.28-2.320.28011590.25442567X-RAY DIFFRACTION99.09
2.32-2.360.2541250.25112606X-RAY DIFFRACTION98.77
2.36-2.40.28741450.24252639X-RAY DIFFRACTION98.83
2.4-2.450.2731420.23752577X-RAY DIFFRACTION99.23
2.45-2.50.26651340.2442641X-RAY DIFFRACTION99.21
2.5-2.550.26351440.22812580X-RAY DIFFRACTION99.09
2.55-2.610.29891210.21522628X-RAY DIFFRACTION98.85
2.61-2.680.2721600.21542594X-RAY DIFFRACTION98.89
2.68-2.750.27241360.21282598X-RAY DIFFRACTION99.09
2.75-2.830.23751380.2092617X-RAY DIFFRACTION98.82
2.83-2.920.22521440.20282597X-RAY DIFFRACTION98.53
2.92-3.030.27191330.20832585X-RAY DIFFRACTION98.55
3.03-3.150.22171260.19332601X-RAY DIFFRACTION98.38
3.15-3.290.21591360.18972583X-RAY DIFFRACTION97.63
3.29-3.470.22181410.18292552X-RAY DIFFRACTION97.86
3.47-3.680.20481320.15822593X-RAY DIFFRACTION97.64
3.68-3.970.16031460.1572580X-RAY DIFFRACTION98.41
3.97-4.370.15881490.14562619X-RAY DIFFRACTION98.89
4.37-50.17891460.14422586X-RAY DIFFRACTION99.6
5-6.290.16831400.1762643X-RAY DIFFRACTION99.78
6.29-42.70.1681500.16272561X-RAY DIFFRACTION97.87
Refinement TLS params.

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

IDL11 (°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)
11.29171875867-0.0461308669330.01325389812841.71169572396-0.2712994478411.454050778950.01680041535790.144747352369-0.1028200475110.02080348834580.04331432237350.1801652773120.189971062058-0.1602568174070.03229740290440.136744007844-0.0838799768946-0.02492993339560.165436227305-0.03623050565740.139213862815-29.5832546677-9.00295968563-7.05048103011
20.968304848385-0.115857228973-0.2374479642531.19939791722-0.3328315113221.152592158440.04085376329910.0552877372497-0.190057568241-0.0839810445466-0.02945210839560.02492282206630.3229064192940.033914071491-0.06065259505460.134913740467-0.0385119351822-0.01402293986010.0861920851561-0.005529021806490.14403508158-16.7693477309-13.9839101976-3.46021658288
32.412767073110.706890390520.2169924976873.119393825120.9855461518992.15255112758-0.014937459053-0.206514298581-0.373495116970.456126922069-0.07407431417090.499647100450.57787162161-0.123428848950.02423126350570.221025190095-0.03289768523320.007343639500190.2138765421060.08982720143810.263963305358-29.2364380196-19.90660662549.38745365956
40.422741849481-0.03795353678330.03961283278540.4768716861880.03610653842810.839198892946-0.0105412882201-0.08457186174530.03949184813190.008554840042830.0204247283371-0.0560889554827-0.05360852709710.0306157113419-0.01616947112870.130684993308-0.0694481866431-0.001768276836330.127475269791-0.001708466173290.144346922263-16.34458672241.273152235854.43813821736
50.9813068269440.04628585413210.09560448114680.656612581876-0.4905142080731.23107887448-0.0214918915647-0.03771779617220.06246545578870.01818609541340.0303250953579-0.0429514739383-0.2397353335370.0334118226819-0.03016760198970.137481609006-0.06960943605480.003013100870360.142555045856-0.009684250431350.13688225585-22.75646625368.80450721203-6.6537532672
61.492727669940.3853180035060.02360476779020.115544350868-0.0716269586920.3360095338160.00467147399856-0.03959696830370.2134999002530.1228560079030.0445515361073-0.12992434399-0.09444215436970.0346224202859-0.01856151722230.230504398107-0.159434318676-0.09343250738530.0133396307987-0.01978031501930.152642720588-13.103357090917.126625962412.9631099215
71.53685235695-0.580390036936-1.067980563292.287938819871.229164665592.40974199208-0.0196660326471-0.08017865636740.09706269098270.07431644120440.113251057089-0.1157167678160.1596601649620.0772881198621-0.08962285474490.0921856742174-0.044852865839-0.02049331847010.1017546083280.006047665751970.115688580271-45.9478363782-11.6942515207-17.6135506656
81.227189966830.35662859918-0.3481979338431.193992785350.04837993893930.4980099046860.052092559645-0.263112828175-0.06258063844840.132391708256-0.0611339597291-0.03819284324640.07712161109540.0429952096025-0.05592983650110.150042538378-0.0681866055936-0.01052987484080.1416551103550.009546914367330.163552813403-50.172687325-4.96287617708-8.56891985917
91.48476088487-0.5520137662860.24426611781.968999568010.9723254148460.669567515299-0.04864692506440.197407876948-0.0149481941342-0.03462810333540.0389329532763-0.01277842924160.0851830414847-0.14610573260.05999904771710.156340607111-0.06463163717160.01426986041210.139991139420.02587407202370.102206196195-52.8041289364-20.0927445777-30.136739794
100.8512420109060.08343232113470.07664681549880.6083617216630.1173478170070.493080826115-0.0441658866927-0.113473222458-0.0216988482991-0.0918075485255-0.03405687175430.1045533599030.0819395921271-0.1297474319290.0759307638920.114192075997-0.0737689284401-0.0109215380440.1733386446130.01052860161930.133817319395-60.4835436742-6.32785169993-22.0412969464
110.6785223916370.01363230444260.3569033819360.6214361460370.09939813743130.924061369209-0.0986212412085-0.002074604893320.105952158545-0.1039934206340.003305473572930.0821874453934-0.1408641992930.03423265650030.09398257598620.167938730806-0.0720162143291-0.01523005890470.134748417788-0.002575804536730.127853351608-56.67376250416.82342842975-27.9346566694
120.4718994964120.2095763267560.0678479493160.453251471479-0.2326521070340.183255253799-0.0298772134694-0.0342182845403-0.01371394837680.1056238169030.0962216952953-0.0455002578173-0.03395821283960.005704035420810.01515623210970.193824718336-0.08746273304440.01379597951380.195285796922-0.04476791456610.135909391087-48.409706852411.3303585981-14.9024825348
136.515930321682.66837001630.08595918861591.851545712040.04173333647130.845452537694-0.3201024711390.09380171714410.446765114205-0.4288054656840.08672739166170.190327904798-0.39649228634-0.07351288754360.1042519810450.379862408813-0.116567801903-0.08907704961110.2193762664850.01704512928190.250958704596-61.648739960416.9933482566-35.8968938339
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 442 through 479 )AA442 - 4791 - 38
22chain 'A' and (resid 480 through 516 )AA480 - 51639 - 75
33chain 'A' and (resid 517 through 537 )AA517 - 53776 - 96
44chain 'A' and (resid 538 through 718 )AA538 - 71897 - 277
55chain 'A' and (resid 719 through 776 )AA719 - 776278 - 335
66chain 'A' and (resid 777 through 797 )AA777 - 797336 - 356
77chain 'B' and (resid 442 through 466 )BE442 - 4661 - 25
88chain 'B' and (resid 467 through 495 )BE467 - 49526 - 54
99chain 'B' and (resid 496 through 537 )BE496 - 53755 - 96
1010chain 'B' and (resid 538 through 616 )BE538 - 61697 - 175
1111chain 'B' and (resid 617 through 746 )BE617 - 746176 - 305
1212chain 'B' and (resid 747 through 776 )BE747 - 776306 - 335
1313chain 'B' and (resid 777 through 797 )BE777 - 797336 - 356

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