5EZY

Crystal structure of T2R-TTL-taccalonolide AJ complex

> Summary

Summary for 5EZY

DescriptorTubulin alpha-1B chain, Tubulin beta-2B chain, Stathmin-4, Uncharacterized protein
Functional Keywordstubulin, complex, inhibitor, structural protein
Biological sourceRattus norvegicus (Rat)
More
Cellular locationCytoplasm, cytoskeleton Q2XVP4 Q6B856
Golgi apparatus  P63043
Total number of polymer chains6
Total molecular weight265748.22
Authors
Wang, Y.,Yu, Y.,Chen, Q.,Yang, J. (deposition date: 2015-11-27, release date: 2017-01-11)
Primary citation
Wang, Y.,Yu, Y.,Chen, Q.,Yang, J.
Microtubule-stabilizing mechanism revealed by taccalonolide AJ-tubulin complex structure
To Be Published,
Experimental method
X-RAY DIFFRACTION (2.05 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.193101.3%5.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5ezy
no rotation
Molmil generated image of 5ezy
rotated about x axis by 90°
Molmil generated image of 5ezy
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, CTubulin alpha-1B chainpolymer45050041.32
UniProt (Q2XVP4)
Pfam (PF00091)
Pfam (PF03953)
Sus scrofa (Pig)Alpha-tubulin ubiquitous,Tubulin K-alpha-1,Tubulin alpha-ubiquitous chain
B, DTubulin beta-2B chainpolymer44549999.92
UniProt (Q6B856)
Pfam (PF00091)
Pfam (PF03953)
Bos taurus (Bovine)
EStathmin-4polymer14316844.21
UniProt (P63043)
Pfam (PF00836)
Rattus norvegicus (Rat)Stathmin-like protein B3,RB3
FUncharacterized proteinpolymer38444378.51
UniProt (E1BQ43)
Pfam (PF03133)
Gallus gallus (Chicken)
GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.23
MAGNESIUM IONnon-polymer24.34
CALCIUM IONnon-polymer40.12
GUANOSINE-5'-DIPHOSPHATEnon-polymer443.21
2-(N-MORPHOLINO)-ETHANESULFONIC ACIDnon-polymer195.22
taccalonolide AJnon-polymer678.72
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTERnon-polymer505.21
waterwater18.01547

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight261305.0
Non-Polymers*Number of molecules15
Total molecular weight4443.2
All*Total molecular weight265748.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.05 Å)

Cell axes105.304158.505180.809
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits45.20 - 2.05
the highest resolution shell value2.074 - 2.050
R-factor0.1883
R-work0.18730
the highest resolution shell value0.261
R-free0.20760
the highest resolution shell value0.287
RMSD bond length0.003
RMSD bond angle0.822

Data Collection Statistics

Resolution limits50.00 - 2.05
the highest resolution shell value -
Number of reflections188559
Rmerge_l_obs0.108
the highest resolution shell value0.789
Completeness99.9
Redundancy6.7
the highest resolution shell value6.9

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC128binding site for residue GTP A 501
ChainResidue
AGLY10
AGLN11
AALA12
AGLN15
AASP98
AALA99
AALA100
AASN101
ASER140
AGLY143
AGLY144
ATHR145
AGLY146
AVAL177
AGLU183
AASN206
ATYR224
AASN228
AILE231
AMG502
AHOH614
AHOH622
AHOH658
AHOH681
AHOH761
AHOH766
AHOH839
BLYS254

AC25binding site for residue MG A 502
ChainResidue
AGTP501
AHOH636
AHOH658
AHOH761
AHOH839

AC35binding site for residue CA A 503
ChainResidue
AASP39
ATHR41
AGLY44
AGLU55
AHOH621

AC424binding site for residue GDP B 501
ChainResidue
BGLY10
BGLN11
BCYS12
BGLN15
BSER140
BGLY143
BGLY144
BTHR145
BGLY146
BPRO173
BVAL177
BASP179
BGLU183
BASN206
BTYR224
BASN228
BMG502
BHOH638
BHOH656
BHOH696
BHOH721
BHOH728
BHOH731
BHOH750

AC56binding site for residue MG B 502
ChainResidue
BGLN11
BGDP501
BHOH615
BHOH708
BHOH750
CHOH843

AC612binding site for residue MES B 503
ChainResidue
BARG158
BPRO162
BASP163
BARG164
BASN197
BTHR198
BASP199
BARG253
BHOH778
BHOH779
BHOH799
BHOH806

AC79binding site for residue MES B 504
ChainResidue
BPHE296
BASP297
BSER298
BARG308
BVAL335
BASN339
BHOH675
BHOH682
BHOH692

AC87binding site for residue TAJ B 505
ChainResidue
BLEU217
BLEU219
BGLY225
BASP226
BHIS229
BTHR276
BARG278

AC930binding site for residue GTP C 501
ChainResidue
CGLY10
CGLN11
CALA12
CGLN15
CASP98
CALA99
CALA100
CASN101
CSER140
CGLY143
CGLY144
CTHR145
CGLY146
CILE171
CVAL177
CGLU183
CASN206
CTYR224
CASN228
CILE231
CMG502
CHOH605
CHOH655
CHOH677
CHOH710
CHOH757
CHOH775
CHOH861
CHOH902
DLYS254

AD15binding site for residue MG C 502
ChainResidue
CGTP501
CHOH657
CHOH677
CHOH861
CHOH902

AD25binding site for residue CA C 503
ChainResidue
CASP39
CTHR41
CGLY44
CGLU55
CHOH618

AD329binding site for residue GTP D 501
ChainResidue
DGLY10
DGLN11
DCYS12
DGLN15
DGLY98
DALA99
DGLY100
DASN101
DSER140
DGLY143
DGLY144
DTHR145
DGLY146
DVAL177
DSER178
DGLU183
DASN206
DTYR224
DASN228
DMG502
DHOH603
DHOH620
DHOH638
DHOH674
DHOH679
DHOH684
DHOH715
DHOH729
DHOH738

AD44binding site for residue MG D 502
ChainResidue
DGTP501
DHOH620
DHOH679
DHOH715

AD511binding site for residue TAJ D 503
ChainResidue
DLEU217
DLEU219
DGLY225
DASP226
DHIS229
DARG278
DGLN282
DGLY370
DHOH624
DHOH714
DHOH726

AD614binding site for residue ACP F 401
ChainResidue
FLYS74
FLYS150
FGLN183
FLYS184
FTYR185
FLEU186
FLYS198
FARG202
FLEU240
FTHR241
FASN242
FASP318
FILE330
FGLU331

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
GTP_5ezy_A_50139GUANOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AVAL9-GLY13GTP: GUANOSINE-5'-TRIPHOSPHATE
AGLN15-ILE16GTP: GUANOSINE-5'-TRIPHOSPHATE
AASP69-LEU70GTP: GUANOSINE-5'-TRIPHOSPHATE
AASP98-ASN102GTP: GUANOSINE-5'-TRIPHOSPHATE
ASER140-SER147GTP: GUANOSINE-5'-TRIPHOSPHATE
AILE171-ALA174GTP: GUANOSINE-5'-TRIPHOSPHATE
AVAL177-ALA180GTP: GUANOSINE-5'-TRIPHOSPHATE
AGLU183GTP: GUANOSINE-5'-TRIPHOSPHATE
AASN206GTP: GUANOSINE-5'-TRIPHOSPHATE
AILE209GTP: GUANOSINE-5'-TRIPHOSPHATE
ATYR224GTP: GUANOSINE-5'-TRIPHOSPHATE
ALEU227-ASN228GTP: GUANOSINE-5'-TRIPHOSPHATE
AILE231GTP: GUANOSINE-5'-TRIPHOSPHATE
BGLN247GTP: GUANOSINE-5'-TRIPHOSPHATE
BLYS254GTP: GUANOSINE-5'-TRIPHOSPHATE

MES_5ezy_B_503152-(N-MORPHOLINO)-ETHANESULFONIC ACID binding site
ChainResidueligand
ATRP407MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BILE154MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BARG158MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BTYR161-MET166MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BGLU196-ASP199MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BARG253MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
ELEU68MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

GDP_5ezy_B_50133GUANOSINE-5'-DIPHOSPHATE binding site
ChainResidueligand
BALA9-GLY13GDP: GUANOSINE-5'-DIPHOSPHATE
BGLN15-ILE16GDP: GUANOSINE-5'-DIPHOSPHATE
BASP69GDP: GUANOSINE-5'-DIPHOSPHATE
BALA99GDP: GUANOSINE-5'-DIPHOSPHATE
BASN101GDP: GUANOSINE-5'-DIPHOSPHATE
BSER140-SER147GDP: GUANOSINE-5'-DIPHOSPHATE
BVAL171GDP: GUANOSINE-5'-DIPHOSPHATE
BPRO173-SER174GDP: GUANOSINE-5'-DIPHOSPHATE
BVAL177-THR180GDP: GUANOSINE-5'-DIPHOSPHATE
BGLU183GDP: GUANOSINE-5'-DIPHOSPHATE
BILE204GDP: GUANOSINE-5'-DIPHOSPHATE
BASN206GDP: GUANOSINE-5'-DIPHOSPHATE
BLEU209GDP: GUANOSINE-5'-DIPHOSPHATE
BTYR224GDP: GUANOSINE-5'-DIPHOSPHATE
BLEU227-ASN228GDP: GUANOSINE-5'-DIPHOSPHATE
BVAL231GDP: GUANOSINE-5'-DIPHOSPHATE

TAJ_5ezy_B_50519taccalonolide AJ binding site
ChainResidueligand
BLYS19TAJ: taccalonolide AJ
BCYS213TAJ: taccalonolide AJ
BLEU217TAJ: taccalonolide AJ
BLEU219TAJ: taccalonolide AJ
BTHR223TAJ: taccalonolide AJ
BGLY225-ASP226TAJ: taccalonolide AJ
BHIS229-LEU230TAJ: taccalonolide AJ
BALA233TAJ: taccalonolide AJ
BPHE272TAJ: taccalonolide AJ
BPRO274-ARG278TAJ: taccalonolide AJ
BARG369-LEU371TAJ: taccalonolide AJ

MES_5ezy_B_504132-(N-MORPHOLINO)-ETHANESULFONIC ACID binding site
ChainResidueligand
BPHE296-LYS299MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BMET301MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BASP306-ARG308MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BTYR312MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BVAL335MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BASN339MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
BTYR342-PHE343MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

GTP_5ezy_C_50141GUANOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
CVAL9-GLY13GTP: GUANOSINE-5'-TRIPHOSPHATE
CGLN15-ILE16GTP: GUANOSINE-5'-TRIPHOSPHATE
CASP69-GLU71GTP: GUANOSINE-5'-TRIPHOSPHATE
CASP98-ASN102GTP: GUANOSINE-5'-TRIPHOSPHATE
CSER140-SER147GTP: GUANOSINE-5'-TRIPHOSPHATE
CILE171-ALA174GTP: GUANOSINE-5'-TRIPHOSPHATE
CVAL177-ALA180GTP: GUANOSINE-5'-TRIPHOSPHATE
CGLU183GTP: GUANOSINE-5'-TRIPHOSPHATE
CVAL204GTP: GUANOSINE-5'-TRIPHOSPHATE
CASN206GTP: GUANOSINE-5'-TRIPHOSPHATE
CILE209GTP: GUANOSINE-5'-TRIPHOSPHATE
CTYR224GTP: GUANOSINE-5'-TRIPHOSPHATE
CLEU227-ASN228GTP: GUANOSINE-5'-TRIPHOSPHATE
CILE231GTP: GUANOSINE-5'-TRIPHOSPHATE
DGLN247GTP: GUANOSINE-5'-TRIPHOSPHATE
DLYS254GTP: GUANOSINE-5'-TRIPHOSPHATE

GTP_5ezy_D_50137GUANOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
DALA9-GLY13GTP: GUANOSINE-5'-TRIPHOSPHATE
DGLN15-ILE16GTP: GUANOSINE-5'-TRIPHOSPHATE
DASP69-GLU71GTP: GUANOSINE-5'-TRIPHOSPHATE
DGLY98-ASN102GTP: GUANOSINE-5'-TRIPHOSPHATE
DSER140-SER147GTP: GUANOSINE-5'-TRIPHOSPHATE
DVAL171GTP: GUANOSINE-5'-TRIPHOSPHATE
DPRO173-SER174GTP: GUANOSINE-5'-TRIPHOSPHATE
DVAL177-SER178GTP: GUANOSINE-5'-TRIPHOSPHATE
DTHR180GTP: GUANOSINE-5'-TRIPHOSPHATE
DGLU183GTP: GUANOSINE-5'-TRIPHOSPHATE
DILE204GTP: GUANOSINE-5'-TRIPHOSPHATE
DASN206GTP: GUANOSINE-5'-TRIPHOSPHATE
DLEU209GTP: GUANOSINE-5'-TRIPHOSPHATE
DTYR224GTP: GUANOSINE-5'-TRIPHOSPHATE
DLEU227-ASN228GTP: GUANOSINE-5'-TRIPHOSPHATE
DVAL231GTP: GUANOSINE-5'-TRIPHOSPHATE

TAJ_5ezy_D_50319taccalonolide AJ binding site
ChainResidueligand
DLYS19TAJ: taccalonolide AJ
DCYS213TAJ: taccalonolide AJ
DLEU217TAJ: taccalonolide AJ
DLEU219TAJ: taccalonolide AJ
DTHR223TAJ: taccalonolide AJ
DGLY225-ASP226TAJ: taccalonolide AJ
DHIS229-LEU230TAJ: taccalonolide AJ
DPHE272TAJ: taccalonolide AJ
DPRO274-ARG278TAJ: taccalonolide AJ
DGLN282TAJ: taccalonolide AJ
DARG369-LEU371TAJ: taccalonolide AJ

ACP_5ezy_F_40121PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER binding site
ChainResidueligand
FLYS74ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FPRO95ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FILE148ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FLYS150ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FGLN183-LEU186ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FLYS198ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FASP200ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FARG202ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FARG222ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FHIS239-ASN242ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FASP318ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FMET320ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FILE330-GLU331ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FASN333ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI21GTP. {ECO:0000255}.
ChainResidueDetails
AGLY142-GLY148

SWS_FT_FI41GTP. {ECO:0000255}.
ChainResidueDetails
CGLY142-GLY148

SWS_FT_FI61ATP analog. {ECO:0000213|PDB:4I4T, ECO:0000213|PDB:4I50, ECO:0000213|PDB: 4I55}.
ChainResidueDetails
FLYS74

SWS_FT_FI71ATP analog. {ECO:0000213|PDB:4TV9}.
ChainResidueDetails
FARG222

SWS_FT_FI81ADP. {ECO:0000213|PDB:4IHJ, ECO:0000213|PDB:4O2A}.
ChainResidueDetails
FGLU331

SWS_FT_FI93ADP. {ECO:0000213|PDB:4IHJ}.
ChainResidueDetails
FLYS74
FLYS150
FLYS198

SWS_FT_FI101ATP analog. {ECO:0000213|PDB:4I55, ECO:0000213|PDB:4O2B, ECO:0000213|PDB: 4O4H}.
ChainResidueDetails
FLYS150

SWS_FT_FI115ATP analog. {ECO:0000213|PDB:4I4T, ECO:0000213|PDB:4I50, ECO:0000213|PDB: 4I55}.
ChainResidueDetails
FGLN183-LEU186
FLYS198-ARG202
FHIS239-ASN242
FASP318-MET320
FGLU331-ASN333

SWS_FT_FI122ADP. {ECO:0000213|PDB:4IHJ, ECO:0000213|PDB:4O2A}.
ChainResidueDetails
FGLN183-LEU186
FTHR241-ASN242

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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