8YUA

Tubulin-RB3-TTL in complex with compound SI10

PDB DOI: https://doi.org/10.2210/pdb8YUA/pdb

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

Deposited: 2024-03-27 Released: 2024-06-05
Deposition Author(s): Wu, C.Y., Wang, Y.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.254
R-Value Work: 0.229
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The complex structure of tubulin-RB3-TTL in complex with compound SI10

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

To be published.

Macromolecule Content

Total Structure Weight: 258.98 kDa
Atom Count: 17,156
Modelled Residue Count: 2,152
Deposited Residue Count: 2,265
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(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
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

Find similar proteins by:

(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 A0A8D0VN39 (Sus scrofa) Explore A0A8D0VN39 Go to UniProtKB: A0A8D0VN39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D0VN39
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	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

Find similar proteins by:

(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 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 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]	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]	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]	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]
A1D69 (Subject of Investigation/LOI) Query on A1D69 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]	N [auth B], S [auth D]	2-chloranyl-~{N}-(4-methoxyphenyl)-~{N}-methyl-thieno[3,2-d]pyrimidin-4-amine C₁₄ H₁₂ Cl N₃ O S HORXFYJUOOLKSX-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]	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]	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]	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]