7E4Y

Crystal structure of tubulin in complex with L-DM4-SMe

PDB DOI: https://doi.org/10.2210/pdb7E4Y/pdb

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

Deposited: 2021-02-16 Released: 2022-02-23
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: 2.71 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198

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: 258.55 kDa
Atom Count: 17,649
Modelled Residue Count: 2,183
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKU (Subject of Investigation/LOI) Query on BKU Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	(1S,2S,3S,5R,6S,16E,18E,20S,21R)-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 (2S)-2-{methyl[3-methyl-3-(methyldisulfanyl)butanoyl]amino}propanoate (non-preferred name) C₃₈ H₅₄ Cl N₃ O₁₀ S₂ SGYGJRKOIZZIEK-TUXWXYFASA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], M [auth C], P [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth C] Focus chain P [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] Interactions & Density Focus chain T [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
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]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C]	I [auth A], O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain S [auth F] MOL2 format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth F] mmCIF format, chain R [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth F]	H [auth A], K [auth B], N [auth C], R [auth D], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth F]