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- PDB-5cb4: Crystal structure of T2R-TTL-Tivantinib complex -

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Basic information

Entry
Database: PDB / ID: 5cb4
TitleCrystal structure of T2R-TTL-Tivantinib complex
Components
  • Stathmin-4
  • Tubulin alpha
  • Tubulin beta
  • Uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / Inhibitor / Complex / Tubulin
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development ...tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / growth cone / microtubule / hydrolase activity / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family ...Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / Dna Ligase; domain 1 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-TIV / Tubulin alpha chain / Tubulin beta chain / Tubulin tyrosine ligase / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus barbatus (bearded pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.193 Å
AuthorsWang, Y. / Yu, Y. / Chen, Q. / Yang, J.
CitationJournal: Febs J. / Year: 2016
Title: Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery.
Authors: Wang, Y. / Zhang, H. / Gigant, B. / Yu, Y. / Wu, Y. / Chen, X. / Lai, Q. / Yang, Z. / Chen, Q. / Yang, J.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha
B: Tubulin beta
C: Tubulin alpha
D: Tubulin beta
E: Stathmin-4
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,92220
Polymers261,3056
Non-polymers3,61714
Water14,934829
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22350 Å2
ΔGint-114 kcal/mol
Surface area80160 Å2
Unit cell
Length a, b, c (Å)105.060, 158.444, 181.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I993*PLUS
#2: Protein Tubulin beta


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I995*PLUS
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 49-189
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
#4: Protein Uncharacterized protein / TUBULIN TYROSINE LIGASE / TTL


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 9 types, 843 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-TIV / (3R,4R)-3-(5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-1-yl)-4-(1H-indol-3-yl)pyrrolidine-2,5-dione / Tivantinib / Tivantinib


Mass: 369.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19N3O2 / Comment: anticancer*YM
#12: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.193→50 Å / Num. obs: 154428 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.193→39.818 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 7677 4.97 %
Rwork0.2073 --
obs0.2085 154411 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→39.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17267 0 230 829 18326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517885
X-RAY DIFFRACTIONf_angle_d0.67624253
X-RAY DIFFRACTIONf_dihedral_angle_d13.7456611
X-RAY DIFFRACTIONf_chiral_restr0.1412634
X-RAY DIFFRACTIONf_plane_restr0.0033139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1928-2.21770.33712110.27083978X-RAY DIFFRACTION82
2.2177-2.24380.29112240.2664906X-RAY DIFFRACTION100
2.2438-2.27110.30562440.2664879X-RAY DIFFRACTION100
2.2711-2.29990.30382670.25884856X-RAY DIFFRACTION100
2.2999-2.33010.27992930.25254878X-RAY DIFFRACTION100
2.3301-2.3620.30692430.25374875X-RAY DIFFRACTION100
2.362-2.39580.2682470.24784886X-RAY DIFFRACTION100
2.3958-2.43150.30062440.23944865X-RAY DIFFRACTION100
2.4315-2.46950.2642980.23884874X-RAY DIFFRACTION100
2.4695-2.510.28282700.24434858X-RAY DIFFRACTION100
2.51-2.55330.29652470.24534875X-RAY DIFFRACTION100
2.5533-2.59970.2872490.24534917X-RAY DIFFRACTION100
2.5997-2.64970.2512610.23194889X-RAY DIFFRACTION100
2.6497-2.70380.27312370.24324879X-RAY DIFFRACTION100
2.7038-2.76250.27312360.24554915X-RAY DIFFRACTION100
2.7625-2.82680.27332540.24414910X-RAY DIFFRACTION100
2.8268-2.89750.2622560.23594899X-RAY DIFFRACTION100
2.8975-2.97580.27032370.2394915X-RAY DIFFRACTION100
2.9758-3.06330.26752940.23324884X-RAY DIFFRACTION100
3.0633-3.16220.25522810.22134881X-RAY DIFFRACTION100
3.1622-3.27510.24032580.23044930X-RAY DIFFRACTION100
3.2751-3.40620.24792580.22464910X-RAY DIFFRACTION100
3.4062-3.56110.22552720.20614928X-RAY DIFFRACTION100
3.5611-3.74870.22152460.19464961X-RAY DIFFRACTION100
3.7487-3.98340.21512520.1854951X-RAY DIFFRACTION100
3.9834-4.29060.18312590.17834951X-RAY DIFFRACTION100
4.2906-4.72180.17982740.15974966X-RAY DIFFRACTION100
4.7218-5.40360.1872710.17085003X-RAY DIFFRACTION100
5.4036-6.80240.22242410.19695074X-RAY DIFFRACTION100
6.8024-39.82440.20572530.18165241X-RAY DIFFRACTION99

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