6TH4 | pdb_00006th4

Tubulin-inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb6TH4/pdb

Classification: CELL CYCLE
Organism(s): Ovis aries, Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-11-18 Released: 2021-12-01
Deposition Author(s): Varela, P.F., Gigant, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.226 (Depositor), 0.238 (DCC)
R-Value Work:
0.192 (Depositor), 0.204 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

B-nor-methylene Colchicinoid PT-100 Selectively Induces Apoptosis in Multidrug-Resistant Human Cancer Cells via an Intrinsic Pathway in a Caspase-Independent Manner

Stein, A., Hilken nee Thomopoulou, P., Frias, C., Hopff, S.M., Varela, P., Wilke, N., Mariappan, A., Neudorfl, J.M., Fedorov, A.Y., Gopalakrishnan, J., Gigant, B., Prokop, A., Schmalz, H.G.

(2022) ACS Omega 7: 2591-2603

DOI: https://doi.org/10.1021/acsomega.1c04659

Macromolecule Content

Total Structure Weight: 220.49 kDa
Atom Count: 14,923
Modeled Residue Count: 1,847
Deposited Residue Count: 1,935
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, C	451	Ovis aries	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	445	Ovis aries	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	143	Rattus norvegicus	Mutation(s): 3 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain G [auth A]	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth C]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain K [auth B] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B]	K [auth B], S [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain S [auth D]
N9B (Subject of Investigation/LOI) Query on N9B Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B]	L [auth B], T [auth D]	1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one C₂₀ H₂₀ O₅ LWZCIQWVGDAJGE-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A] I [auth B] J [auth B] M [auth C] N [auth C] F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain H [auth A] MOL2 format, chain P [auth D] MOL2 format, chain H [auth A] mmCIF format, chain P [auth D] mmCIF format, chain H [auth A]	H [auth A], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain P [auth D]