6z81

TsaBD bound to the inhibitor

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

tRNA N6-adenosine threonylcarbamoyltransferase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	tRNA threonylcarbamoyladenosine biosynthesis protein TsaB × 1 （P76256） NICKEL (II) ION × 2 ZINC ION × 1 ;(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid ; × 1 SULFATE ION × 2 SODIUM ION × 2 ACETATE ION × 6 DI(HYDROXYETHYL)ETHER × 2 ADENOSINE MONOPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	tRNA threonylcarbamoyladenosine biosynthesis protein TsaB × 1 （P76256） NICKEL (II) ION × 2 ZINC ION × 1 ;(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid ; × 1 SULFATE ION × 2 SODIUM ION × 1 ACETATE ION × 3 DI(HYDROXYETHYL)ETHER × 1 ADENOSINE MONOPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TSAD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 1–337 Author chain B； PDBConstruct 1–337； UniProt 1–337

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

Escherichia coli

UniProt P76256

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	tRNA N6-adenosine threonylcarbamoyltransferase × 1 （P05852） NICKEL (II) ION × 2 ZINC ION × 1 ;(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid ; × 1 SULFATE ION × 2 SODIUM ION × 2 ACETATE ION × 6 DI(HYDROXYETHYL)ETHER × 2 ADENOSINE MONOPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	tRNA N6-adenosine threonylcarbamoyltransferase × 1 （P05852） NICKEL (II) ION × 2 ZINC ION × 1 ;(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid ; × 1 SULFATE ION × 2 SODIUM ION × 1 ACETATE ION × 3 DI(HYDROXYETHYL)ETHER × 1 ADENOSINE MONOPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TSAB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–231； UniProt 1–231 Author chain D； PDBConstruct 1–231； UniProt 1–231

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6z81
Deposition date deposition_date	2020-06-02
Structure title title	TsaBD bound to the inhibitor
Keywords keywords	tRNA TsaB TsaD, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6z81__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6z81__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z81__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.99 Å
Rg (electron density)	27.20 Å
Total Rg	27.85 Å
Atom count	4374
Residues	569
Excluded volume	77729 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z81__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6z81__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	tRNA N6-adenosine threonylcarbamoyltransferase
Molecular weight formula_weight	36879.2 kDa
EC 编号 ec_number	2.3.1.234
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8886

MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPAAHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Molecular weight formula_weight	26033.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLPGKEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid ;
Molecular weight formula_weight	490.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 9 Entity 9 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6z81c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d6z81c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d6z81d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d6z81d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

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Unit-cell length a length_a	63.230 Å
Unit-cell length b length_b	69.250 Å
Unit-cell length c length_c	86.540 Å
Unit-cell angle α angle_alpha	109.38 °
Unit-cell angle β angle_beta	92.00 °
Unit-cell angle γ angle_gamma	116.94 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	42.470 Å
R factor r_factor	0.1850
R_work r_work	0.1820
R_free r_free	0.2330

TsaBD bound to the inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

tRNA N6-adenosine threonylcarbamoyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6z81__assembly_2__model_1

6z81__assembly_2__model_1 | I(q)

6z81__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

TsaBD bound to the inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

tRNA N6-adenosine threonylcarbamoyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6z81__assembly_2__model_1

6z81__assembly_2__model_1 | I(q)

6z81__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)