8YEM | pdb_00008yem

Tubulin-RB3_SLD-TTL in complex with compound 9

PDB DOI: https://doi.org/10.2210/pdb8YEM/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Sus scrofa, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-02-26
Deposition Author(s): Wu, C.Y., Wang, Y.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.284 (Depositor), 0.282 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

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-RB3_SLD-TTL in complex with compound 9

Wu, C.Y., Wang, Y.X.

To be published.

Macromolecule Content

Total Structure Weight: 258.32 kDa
Atom Count: 17,399
Modeled Residue Count: 2,174
Deposited Residue Count: 2,258
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1B chain	A, C	440	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
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	431	Sus scrofa	Mutation(s): 0 Gene Names: TUBB2B
UniProt
Find proteins for A0A287AGU7 (Sus scrofa) Explore A0A287AGU7 Go to UniProtKB: A0A287AGU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A287AGU7
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	136	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 EC: 6.3.2.25
UniProt
Find proteins for A0A8C9FGJ1 (Pavo cristatus) Explore A0A8C9FGJ1 Go to UniProtKB: A0A8C9FGJ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8C9FGJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain O [auth C]	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]
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] SDF format, chain R [auth D] MOL2 format, chain J [auth B] MOL2 format, chain R [auth D] mmCIF format, chain J [auth B] mmCIF format, chain R [auth D]	J [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain R [auth D]
A1D6D (Subject of Investigation/LOI) Query on A1D6D Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain S [auth D] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D]	N [auth B], S [auth D]	4-(2-chloranyl-6-fluoranyl-quinazolin-4-yl)-7-methoxy-1,3-dihydroquinoxalin-2-one C₁₇ H₁₂ Cl F N₄ O₂ CKELETCMFVMWNT-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain S [auth D] Interactions & Density Focus chain N [auth B] Focus chain S [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C]	H [auth A], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain P [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	I [auth A], M [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C]