9LNL | pdb_00009lnl

Crystal structure of T2R-TTL-YQVB15 complex

PDB DOI: https://doi.org/10.2210/pdb9LNL/pdb

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

Deposited: 2025-01-21 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: 2.85 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (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-YQVB15 complex

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

To be published.

Macromolecule Content

Total Structure Weight: 264.24 kDa
Atom Count: 17,558
Modelled Residue Count: 2,182
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, 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% 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-2B chain	C [auth D], F [auth B]	445	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	D [auth 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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EPQ (Subject of Investigation/LOI) Query on A1EPQ Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	10',11'-difluoro-12'-methoxyvinblastine C₄₇ H₅₈ F₂ N₄ O₁₀ VGIXSHDRLZHSPP-PEAUBOKCSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C]	G [auth A], I [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth C]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain O [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth B]	M [auth D], O [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain M [auth D] Focus chain O [auth B] Interactions & Density Focus chain M [auth D] Focus chain O [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C]	H [auth A], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain N [auth B] MOL2 format, chain J [auth C] MOL2 format, chain N [auth B] mmCIF format, chain J [auth C] mmCIF format, chain N [auth B]	J [auth C], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain N [auth B] Interactions & Density Focus chain J [auth C] Focus chain N [auth B]