8YRK | pdb_00008yrk

Tubulin-Compound KY216: stathmin-like domain complex

PDB DOI: https://doi.org/10.2210/pdb8YRK/pdb

Classification: CELL CYCLE
Organism(s): Sus scrofa, Mus musculus, Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-21 Released: 2025-04-02
Deposition Author(s): Xia, Y.Z., He, X.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.226 (Depositor), 0.225 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Tubulin-Compound KY216: stathmin-like domain complex

Xia, Y.Z., He, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 265.37 kDa
Atom Count: 17,720
Modelled Residue Count: 2,191
Deposited Residue Count: 2,317
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	450	Sus scrofa	Mutation(s): 0 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	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1UIR5 (Sus scrofa) Explore A0A8D1UIR5 Go to UniProtKB: A0A8D1UIR5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1UIR5
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	Mus musculus	Mutation(s): 0 Gene Names: Stmn4
UniProt & NIH Common Fund Data Resources
Find proteins for P63042 (Mus musculus) Explore P63042 Go to UniProtKB: P63042
IMPC: MGI:1931224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63042
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(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 Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth C]	G [auth A], Q [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain Q [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain X [auth F] MOL2 format, chain X [auth F] mmCIF format, chain X [auth F]	X [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain X [auth F] Interactions & Density Focus chain X [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain K [auth B] MOL2 format, chain U [auth D] MOL2 format, chain K [auth B] mmCIF format, chain U [auth D] mmCIF format, chain K [auth B]	K [auth B], U [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain U [auth D] Interactions & Density Focus chain K [auth B] Focus chain U [auth D]
A1D62 (Subject of Investigation/LOI) Query on A1D62 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D] mmCIF format, chain P [auth B] mmCIF format, chain W [auth D]	P [auth B], W [auth D]	(11R,16S)-11-(3,5-dichloro-4-methoxyphenyl)-4,7-dioxa-12,14-diazatetracyclo[8.7.0.03,8.012,16]heptadeca-1,3(8),9-triene-13,15-dione C₂₀ H₁₆ Cl₂ N₂ O₅ GANPPQNYXDZLNS-WMLDXEAASA-N		Interactions Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain P [auth B] Focus chain W [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C]	I [auth A], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain R [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 L [auth B] SDF format, chain T [auth D] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain V [auth D]	H [auth A], L [auth B], T [auth D], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain T [auth D] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain T [auth D] Focus chain V [auth D]