5Z4U | pdb_00005z4u

Crystal Structure of T2R-TTL complex with 7a3

PDB DOI: https://doi.org/10.2210/pdb5Z4U/pdb

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

Deposited: 2018-01-14 Released: 2019-01-23
Deposition Author(s): Lai, Q., Wang, Y., Yang, J., Yao, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.235 (Depositor), 0.234 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of T2R-TTL complex with 7a3

Lai, Q., Wang, Y., Yang, J., Yao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 265.04 kDa
Atom Count: 17,352
Modeled Residue Count: 2,151
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
Tubulin alpha-1B chain	A, 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-2B chain	B, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 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

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 S [auth D] SDF format, chain P [auth C] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain G [auth A]	G [auth A], P [auth C], S [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
96C Query on 96C Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain O [auth B] mmCIF format, chain U [auth D] mmCIF format, chain O [auth B]	O [auth B], U [auth D]	4-(4-ethoxyphenyl)-1-methyl-3-(3,4,5-trimethoxyphenyl)-1H-pyrazole C₂₁ H₂₄ N₂ O₄ YWYCRTNRTJCKHS-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain O [auth B] Focus chain U [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B]	L [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain L [auth B] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], Q [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.235 (Depositor), 0.234 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.491	α = 90
b = 158.233	β = 90
c = 182.099	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

5Z4U | pdb_00005z4u

Crystal Structure of T2R-TTL complex with 7a3

Literature

Crystal Structure of T2R-TTL complex with 7a3

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)