8WMU

Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites

• PDB DOI: https://doi.org/10.2210/pdb8WMU/pdb

• Classification: CELL CYCLE
• Organism(s): Sus scrofa, Rattus norvegicus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-04 Released: 2024-10-09 
• Deposition Author(s): Zhao, W., Bi, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Starting Model: in silico

Literature

Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites

Zhao, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 258.49 kDa 
• Atom Count: 17,170 
• Modelled Residue Count: 2,149 
• Deposited Residue Count: 2,260 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1B chain	A, C	440	Sus scrofa	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	431	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0VN39 (Sus scrofa) Explore A0A8D0VN39  Go to UniProtKB:  A0A8D0VN39

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	138	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin--tyrosine ligase	F	380	Gallus gallus	Mutation(s): 0  EC: 6.3.2.25
UniProt
Find proteins for A0A8C9FGJ1 (Pavo cristatus) Explore A0A8C9FGJ1  Go to UniProtKB:  A0A8C9FGJ1

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D55 (Subject of Investigation/LOI)	O [auth B]	(5~{S},5~{a}~{S},8~{a}~{R},9~{R})-5-(quinolin-6-ylamino)-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one C31 H28 N2 O7 CKAQZFBCKGLIQY-MHTDFPPDSA-N
GTP	G [auth A], P [auth C], T [auth D]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	L [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	K [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	S [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	I [auth A], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], M [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.572	α = 90
b = 157.618	β = 90
c = 179.348	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Zhao, W., Bi, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release