9LNX | pdb_00009lnx

Crystal structure of T2R-TTL-YQVB9 Complex

PDB DOI: https://doi.org/10.2210/pdb9LNX/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Sus scrofa, Mus musculus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-22 Released: 2025-05-07
Deposition Author(s): Wu, C.Y., Wang, Y.X., Chen, Q.F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.296 (Depositor), 0.298 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (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

Crystal structure of T2R-TTL-YQVB9 Complex

Wu, C.Y., Wang, Y.X., Chen, Q.F.

To be published.

Macromolecule Content

Total Structure Weight: 264.21 kDa
Atom Count: 17,557
Modeled Residue Count: 2,182
Deposited Residue Count: 2,317
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1B chain	A, B [auth C]	450	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	C [auth D], F [auth B]	445	Sus scrofa	Mutation(s): 0 Gene Names: TUBB2B, LOC100624785
UniProt
Find proteins for A0A8D1UIR5 (Sus scrofa) Explore A0A8D1UIR5 Go to UniProtKB: A0A8D1UIR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1UIR5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	D [auth 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63042
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	E [auth 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EPT (Subject of Investigation/LOI) Query on A1EPT Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	10'-methoxyvinblastine C₄₇ H₆₀ N₄ O₁₀ ZHXGWQQGBFGQPC-SYWRHQDJSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth D]	N [auth D], O [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain N [auth D] Focus chain O [auth B] Interactions & Density Focus chain N [auth D] Focus chain O [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	I [auth A], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A]	H [auth A], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth C]