Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents
Zhao, W.To be published.
Experimental Data Snapshot
Starting Model: in silico
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Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Detyrosinated tubulin alpha-1B chain | 440 | Sus scrofa | Mutation(s): 0  EC: 3.6.5 | ||
UniProt | |||||
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2XVP4 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Tubulin beta chain | 445 | Sus scrofa | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for A0A8D1UIR5 (Sus scrofa) Explore A0A8D1UIR5  Go to UniProtKB:  A0A8D1UIR5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A8D1UIR5 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Stathmin-4 | 138 | Rattus norvegicus | Mutation(s): 0  Gene Names: Stmn4 | ||
UniProt | |||||
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P63043 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Tubulin--tyrosine ligase | 381 | Gallus gallus | Mutation(s): 0  EC: 6.3.2.25 | ||
UniProt | |||||
Find proteins for A0A8C9FGJ1 (Pavo cristatus) Explore A0A8C9FGJ1  Go to UniProtKB:  A0A8C9FGJ1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A8C9FGJ1 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 9 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GTP Query on GTP | G [auth A], P [auth C], W [auth D] | GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N | |||
WIW (Subject of Investigation/LOI) Query on WIW | N [auth B] | (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one C26 H24 N2 O7 S VJWQXPQIWVFAAY-JNTAVDMJSA-N | |||
ACP Query on ACP | AA [auth F] | PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N | |||
GDP Query on GDP | K [auth B] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N | |||
MES Query on MES | M [auth B] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N | |||
PEG Query on PEG | J [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
EDO Query on EDO | I [auth A] O [auth B] S [auth C] T [auth C] U [auth C] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CA Query on CA | R [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | H [auth A], L [auth B], Q [auth C], X [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 103.82 | α = 90 |
b = 156.446 | β = 90 |
c = 179.393 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |
Funding Organization | Location | Grant Number |
---|---|---|
Ministry of Science and Technology (MoST, China) | China | 2019YFA0905700 |