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- PDB-9mlf: TUBULIN-RB3_SLD IN COMPLEX WITH COMPOUND QW-4-183-llb -

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Basic information

Entry
Database: PDB / ID: 9mlf
TitleTUBULIN-RB3_SLD IN COMPLEX WITH COMPOUND QW-4-183-llb
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / STRUCTURAL PROTEIN/INHIBITOR / MICROTUBULE INHIBITOR / COLCHICINE / CANCER / CELL CYCLE INHIBITOR COMPLEX / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / microtubule depolymerization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site ...Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
: / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMiller, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Design and synthesis of novel 4-aryl-2-benzoyl-imidazoles as colchicine binding site inhibitors.
Authors: Albadari, N. / Xie, Y. / Wang, Q. / Miller, D.J. / Gruntz, J.Q. / Oldham, M.L. / Chen, H. / Ma, D. / Wu, Z. / Miller, D.D. / Li, W.
History
DepositionDec 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,51713
Polymers211,7095
Non-polymers2,8088
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-124 kcal/mol
Surface area63340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.482, 126.974, 252.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48780.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 48648.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16851.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

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Non-polymers , 6 types, 247 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-A1BMG / [(4M)-4-(1H-indol-4-yl)-1H-imidazol-2-yl](3,4,5-trimethoxyphenyl)methanone


Mass: 377.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M trisodium citrate, pH 5.6, 0.2 M ammonium sulfate, 12.2% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92012 Å / Relative weight: 1
ReflectionResolution: 2.4→34.35 Å / Num. obs: 84508 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.997 / Rsym value: 0.156 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.5 % / Num. unique obs: 4420 / CC1/2: 0.639 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.35 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 4204 4.99 %
Rwork0.1985 --
obs0.2002 84193 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14257 0 182 239 14678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.673
X-RAY DIFFRACTIONf_dihedral_angle_d15.8915399
X-RAY DIFFRACTIONf_chiral_restr0.0442192
X-RAY DIFFRACTIONf_plane_restr0.0052607
LS refinement shellResolution: 2.4→2.43 Å
RfactorNum. reflection% reflection
Rfree0.3099 143 -
Rwork0.2784 2613 -
obs--100 %
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)
10.10770.03020.1011-0.0273-0.04550.0074-0.0375-0.0825-0.12010.09470.03440.07970.0237-0.004200.3483-0.00390.00570.32230.03830.314-15.1242-27.510660.1424
20.02680.07330.02680.0478-0.01330.07050.0169-0.1142-0.02740.01340.04260.11120.0133-0.117400.468-0.00730.0640.40620.04420.3762-20.2906-28.852571.2385
30.0156-0.0282-0.08280.02520.00940.01630.0636-0.03030.26050.1750.11260.2352-0.22320.116100.52840.00930.09650.28270.03330.3287-13.6418-15.732362.7238
40.31310.1044-0.11960.16350.1137-0.03250.0245-0.1741-0.04350.268-0.1348-0.1475-0.24750.11750.00010.4175-0.0331-0.01240.36380.03710.23071.1489-17.958560.233
5-0.03130.0611-0.26870.42180.1960.2187-0.0579-0.043-0.1338-0.0782-0.0588-0.09330.07230.1429-00.27690.00680.00590.26790.07010.2479-1.17-27.676352.2786
60.11520.0927-0.09460.06880.01330.0679-0.15870.1443-0.0337-0.22040.13030.09310.0202-0.017600.459-0.0527-0.08290.3560.06420.3755-18.8394-27.542440.4387
70.16760.17-0.02220.08180.047-0.0156-0.1956-0.08640.11290.12750.10710.04010.2692-0.0587-00.3856-0.02070.00660.420.03630.4261-15.479-36.635555.454
80.00080.12020.1540.41440.2176-0.2509-0.06770.13510.0467-0.29090.02580.14730.2856-0.003-00.4542-0.0581-0.03480.37780.05590.3837-15.7961-40.711741.7761
90.01090.0777-0.02730.025-0.0183-0.02240.3591-0.2249-0.1826-0.2116-0.02790.32370.43980.03280.0230.6481-0.2257-0.25310.29280.15810.6379-21.6274-50.252546.4183
100.14010.2590.13710.21540.0180.2229-0.01240.0680.0316-0.17540.10880.15640.3727-0.132700.5902-0.04910.03460.4240.10450.5541-19.8324-43.836148.4019
110.0795-0.24880.0990.0701-0.2546-0.0499-0.03510.087-0.0279-0.31250.0618-0.03730.2288-0.04510.00180.5549-0.03890.01940.24990.02130.2563-4.3692-32.891538.0145
120.1634-0.00590.22440.0644-0.04210.24610.0328-0.0193-0.0688-0.2693-0.2584-0.39570.10770.1285-0.00580.42590.03160.09820.29670.06930.31848.3561-27.217440.0844
130.5772-0.15170.30910.0943-0.10570.3235-0.047-0.17640.23960.2713-0.02310.2512-0.1526-0.11600.4705-0.00570.15030.3043-0.04210.4128-10.636113.833746.5703
140.23850.10240.17980.2216-0.06650.2150.0818-0.08990.19940.5459-0.4687-0.36-0.35220.3318-0.07310.7629-0.09850.00350.2652-0.07380.2077.816419.807545.7505
150.38470.51990.17840.85170.2023-0.07450.0661-0.01350.1038-0.0088-0.03630.15170.13880.0347-00.3873-0.02-0.00670.26610.03120.24872.611810.333833.4483
160.1210.25510.03090.1310.01360.1236-0.010.0290.14390.2294-0.11720.02850.14280.0035-0.00630.2939-0.01710.00850.27780.02520.3307-8.68481.807937.9889
170.17040.25280.11780.1570.0746-0.009-0.37290.03170.20610.05370.20510.0558-0.04420.12420.00180.4254-0.068-0.00560.31250.06620.3043-8.5581-0.914327.5635
180.13570.10930.07330.3432-0.1358-0.1238-0.09760.0801-0.0106-0.23870.11150.29380.15160.04910.00020.4347-0.0626-0.04650.30470.05580.38-11.7783-7.330327.2936
190.0498-0.2538-0.13590.20930.021-0.0368-0.1850.03960.0717-0.37220.17690.00820.22180.002200.4215-0.05540.02690.29650.02370.24986.29875.923621.6915
200.0744-0.06180.06420.0954-0.16330.33890.01230.0141-0.1015-0.0749-0.0987-0.40470.15040.09400.38020.00760.04520.32060.0420.335416.45727.166825.6652
210.56650.1842-0.27550.4798-0.13680.5635-0.0182-0.00440.03910.255-0.07050.0569-0.14050.0788-0.00010.3779-0.06790.04790.25660.02040.236316.327851.048931.5546
220.10460.36250.08420.79520.0278-0.0547-0.12230.00190.2086-0.25250.09420.17520.31550.0375-0.00420.3457-0.0638-0.00890.33740.04490.37893.746340.338117.1061
230.18590.34160.01730.4839-0.31410.2599-0.1169-0.00670.0174-0.16250.014-0.02450.17290.0157-0.00410.3413-0.0290.04150.27850.03020.301817.808740.759713.9491
240.6282-0.20190.48070.13160.03840.5172-0.0358-0.43640.35130.4317-0.1015-0.0929-0.3816-0.199-0.03640.348-0.00960.04190.4314-0.08580.354629.218789.233521.0816
250.47330.2342-0.24450.30490.36750.32330.0766-0.1645-0.09010.2074-0.2663-0.2213-0.02210.124-0.01760.1748-0.0783-0.04180.37940.09480.292243.478380.639515.6403
260.33780.14680.22990.39220.20150.2143-0.0031-0.06610.1510.009-0.0595-0.05210.1363-0.0938-0.03030.13640.00230.00930.32270.06740.297529.064878.72025.5651
270.28460.15720.04940.0471-0.03570.2655-0.25230.11360.2786-0.22140.13790.16620.3819-0.2798-0.0340.0748-0.0112-0.0870.35560.06470.440921.291778.7996-3.9118
280.0828-0.00480.05660.1070.01190.0639-0.26410.0413-0.01270.03910.05250.2223-0.0309-0.0268-0.05070.1583-0.07530.01530.37790.00510.356215.345768.34321.7668
290.16140.12580.0950.0364-0.03220.11650.0486-0.0615-0.0198-0.18310.0930.23030.2463-0.20140.00030.216-0.010.00410.32620.04640.356720.534568.60733.1522
300.098-0.02010.1280.27890.05740.0581-0.0460.22230.1261-0.16250.0631-0.01460.0285-0.0604-0.00320.1429-0.00590.02390.30290.05440.298440.83876.1628-2.8566
310.14810.11440.02940.03860.0735-0.0183-0.2274-0.1256-0.2336-0.3774-0.3987-0.64691.7573-0.211-0.2188-0.46410.3324-0.10770.23570.25230.53851.821373.59061.4601
320.1004-0.10070.19250.1148-0.08090.0945-0.1491-0.3126-0.27190.18710.11910.09430.56290.134800.7523-0.0250.10510.50760.09790.6886-11.9236-55.182152.2357
33-0.08360.2589-0.10760.1244-0.2436-0.15080.045-0.0998-0.137-0.0031-0.2452-0.33650.02480.169-0.04260.5921-0.1155-0.05490.52930.20590.601334.665730.636336.3285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 199 )
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 223 )
7X-RAY DIFFRACTION7chain 'A' and (resid 224 through 259 )
8X-RAY DIFFRACTION8chain 'A' and (resid 260 through 311 )
9X-RAY DIFFRACTION9chain 'A' and (resid 312 through 338 )
10X-RAY DIFFRACTION10chain 'A' and (resid 339 through 372 )
11X-RAY DIFFRACTION11chain 'A' and (resid 373 through 401 )
12X-RAY DIFFRACTION12chain 'A' and (resid 402 through 437 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 86 )
14X-RAY DIFFRACTION14chain 'B' and (resid 87 through 125 )
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 221 )
16X-RAY DIFFRACTION16chain 'B' and (resid 222 through 257 )
17X-RAY DIFFRACTION17chain 'B' and (resid 258 through 294 )
18X-RAY DIFFRACTION18chain 'B' and (resid 295 through 363 )
19X-RAY DIFFRACTION19chain 'B' and (resid 364 through 391 )
20X-RAY DIFFRACTION20chain 'B' and (resid 392 through 430 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 199 )
22X-RAY DIFFRACTION22chain 'C' and (resid 200 through 337 )
23X-RAY DIFFRACTION23chain 'C' and (resid 338 through 438 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 100 )
25X-RAY DIFFRACTION25chain 'D' and (resid 101 through 197 )
26X-RAY DIFFRACTION26chain 'D' and (resid 198 through 271 )
27X-RAY DIFFRACTION27chain 'D' and (resid 272 through 309 )
28X-RAY DIFFRACTION28chain 'D' and (resid 310 through 336 )
29X-RAY DIFFRACTION29chain 'D' and (resid 337 through 362 )
30X-RAY DIFFRACTION30chain 'D' and (resid 363 through 391 )
31X-RAY DIFFRACTION31chain 'D' and (resid 392 through 430 )
32X-RAY DIFFRACTION32chain 'E' and (resid 6 through 46 )
33X-RAY DIFFRACTION33chain 'E' and (resid 47 through 139 )

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