9GNU | pdb_00009gnu

Tubulin in complex with a dioxane analog of zampanolide

PDB DOI: https://doi.org/10.2210/pdb9GNU/pdb

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

Deposited: 2024-09-04 Released: 2025-09-17
Deposition Author(s): Oliva, M.A., Diaz, J.F., Altmann, K.H.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)

Starting Model: experimental
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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

Tubulin in complex with a dioxane analog of zampanolide

Oliva, M.A., Diaz, J.F., Altmann, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 271.19 kDa
Atom Count: 18,510
Modeled Residue Count: 2,152
Deposited Residue Count: 2,365
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	189	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	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus) Explore A0A8V0Z8P0 Go to UniProtKB: A0A8V0Z8P0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	G [auth A], S [auth C], W [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain S [auth C] Focus chain W [auth D]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain Z [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain Z [auth F]	Z [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Z [auth F] Interactions & Density Focus chain Z [auth F]
A1IND (Subject of Investigation/LOI) Query on A1IND Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Y [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth D]	R [auth B], Y [auth D]	(2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide C₂₇ H₃₅ N O₇ NOKRNQYEWWLQEJ-KHFBQCEVSA-N		Interactions Focus chain R [auth B] Focus chain Y [auth D] Interactions & Density Focus chain R [auth B] Focus chain Y [auth D]
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [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]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	L [auth A], O [auth B], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain V [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C]	I [auth A], K [auth A], Q [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain U [auth C]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		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 AA [auth F] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	AA [auth F], H [auth A], P [auth B], T [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.197	α = 90
b = 159.166	β = 90
c = 178.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Oliva, M.A.

Diaz, J.F.

Altmann, K.H.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	CNS2023-145079
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-123399OB-I00
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-136765OB-I00