8WMU | pdb_00008wmu

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Zhao, W.

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 A0A8D1UIR5 (Sus scrofa) Explore A0A8D1UIR5 Go to UniProtKB: A0A8D1UIR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1UIR5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8C9FGJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D55 (Subject of Investigation/LOI) Query on A1D55 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	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		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain G [auth A]	G [auth A], P [auth C], T [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain T [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F] mmCIF format, chain U [auth F]	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A]	I [auth A], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain R [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C]