9GMY | pdb_00009gmy

Tubulin in complex with an oxathiane analog of zampanolide

PDB DOI: https://doi.org/10.2210/pdb9GMY/pdb

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

Deposited: 2024-08-30 Released: 2025-09-10
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: 1.97 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (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 an oxathiane analog of zampanolide

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

To be published.

Macromolecule Content

Total Structure Weight: 271.08 kDa
Atom Count: 18,956
Modeled Residue Count: 2,145
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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(by identity cutoff) | 3D Structure

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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(by identity cutoff) | 3D Structure

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 10 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 R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain R [auth C]	G [auth A], R [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain R [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Y [auth F]	Y [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]
A1IM9 (Subject of Investigation/LOI) Query on A1IM9 Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain X [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth D]	Q [auth B], X [auth D]	(2Z,4E)-N-[(S)-[(1R,2E,5S,8E,10Z,17S)-3,11-dimethyl-7,13-bis(oxidanylidene)-6,21-dioxa-19-thiabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl]-oxidanyl-methyl]hexa-2,4-dienamide C₂₇ H₃₇ N O₆ S AYYLWQFSMNQBEY-JBPAPXCVSA-N		Interactions Focus chain Q [auth B] Focus chain X [auth D] Interactions & Density Focus chain Q [auth B] Focus chain X [auth D]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain V [auth D] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D] mmCIF format, chain L [auth B] mmCIF format, chain V [auth D]	L [auth B], V [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain V [auth D]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	K [auth A], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C]	I [auth A], P [auth B], T [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain T [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain T [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 H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth F]	H [auth A], M [auth B], S [auth C], W [auth D], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth F]