7E4P

Crystal structure of tubulin in complex with Ansamitocin P3

PDB DOI: https://doi.org/10.2210/pdb7E4P/pdb

Classification: STRUCTURAL PROTEIN/INHIBITOR
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-14 Released: 2022-02-16
Deposition Author(s): Wang, Y., Li, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.229
R-Value Work: 0.213
R-Value Observed: 0.213

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

C3 Ester Side Chain Plays a Pivotal Role in the Antitumor Activity of Maytansinoids

Wang, Y., Li, W.

To be published.

Macromolecule Content

Total Structure Weight: 258.47 kDa
Atom Count: 18,225
Modelled Residue Count: 2,182
Deposited Residue Count: 2,260
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	440	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	431	Bos taurus	Mutation(s): 0 Gene Names: TUBB2B
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	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 Gene Names: TTL
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKF (Subject of Investigation/LOI) Query on BKF Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate C₃₂ H₄₃ Cl N₂ O₉ OPQNCARIZFLNLF-GFSDGHFRSA-N		Interactions Focus chain R [auth D]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	G [auth A], N [auth C], Q [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain Q [auth D]
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]
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B]
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]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C]	I [auth A], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain U [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth F]	H [auth A], L [auth B], O [auth C], S [auth D], U [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth F]