9IXB | pdb_00009ixb

Structure of tubulin and nitrogen-containing heterocyclic substituted podophyllotoxin derivatives complex

PDB DOI: https://doi.org/10.2210/pdb9IXB/pdb

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

Deposited: 2024-07-27 Released: 2025-07-30
Deposition Author(s): Bi, J., Zhao, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.48 Å
R-Value Free:
0.267 (Depositor), 0.266 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.224 (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

Structure of tubulin and nitrogen-containing heterocyclic substituted podophyllotoxin derivatives complex

Bi, J.

To be published.

Macromolecule Content

Total Structure Weight: 258.09 kDa
Atom Count: 15,844
Modeled Residue Count: 2,109
Deposited Residue Count: 2,258
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	430	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A480UE93 (Sus scrofa) Explore A0A480UE93 Go to UniProtKB: A0A480UE93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A480UE93
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ECQ (Subject of Investigation/LOI) Query on A1ECQ Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	(5~{S},5~{a}~{S},8~{a}~{R},9~{R})-5-(1~{H}-indazol-5-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 C₂₉ H₂₇ N₃ O₇ AUUVOEBQGAGZHB-DWJNZRAMSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C]	G [auth A], P [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain P [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain T [auth F] MOL2 format, chain T [auth F] mmCIF format, chain T [auth F]	T [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain T [auth F] Interactions & Density Focus chain T [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain S [auth D] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D]	N [auth B], S [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain N [auth B] Focus chain S [auth D] Interactions & Density Focus chain N [auth B] Focus chain S [auth D]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C]	I [auth A], O [auth B], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]