2hdn

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

Method: X-RAY DIFFRACTION

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

Elongation factor EF-Tu

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TETRACYCLINE × 1 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 TETRACYCLINE × 2 water × 4	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 TETRACYCLINE × 2 water × 4	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 TETRACYCLINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFTU_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–37； UniProt 8–44 Author chain C； PDBConstruct 1–37； UniProt 8–44 Author chain E； PDBConstruct 1–37； UniProt 8–44 Author chain G； PDBConstruct 1–37； UniProt 8–44 Author chain I； PDBConstruct 1–37； UniProt 8–44 Author chain K； PDBConstruct 1–37； UniProt 8–44 Author chain B； PDBConstruct 1–335； UniProt 59–393 Author chain D； PDBConstruct 1–335； UniProt 59–393 Author chain F； PDBConstruct 1–335； UniProt 59–393 Author chain H； PDBConstruct 1–335； UniProt 59–393 Author chain J； PDBConstruct 1–335； UniProt 59–393 Author chain L； PDBConstruct 1–335； UniProt 59–393

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	2hdn
Deposition date deposition_date	2006-06-20
Structure title title	Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution
Keywords keywords	trypsin-modified EF-Tu, GTPase center, complex with tetracycline, TRANSLATION; TRANSLATION
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.

2hdn__assembly_1__model_1

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

Download this curve (.dat)

2hdn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hdn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.51 Å
Rg (electron density)	23.73 Å
Total Rg	24.59 Å
Atom count	2894
Residues	368
Excluded volume	51625 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hdn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hdn__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2hdn__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2hdn__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2hdn__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2hdn__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2hdn__assembly_7__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2hdn__assembly_8__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2hdn__assembly_9__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Elongation factor EF-Tu
Molecular weight formula_weight	3765.3 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	17608

TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAAR

Entity 2 Entity 2 polymer

Description description	Elongation factor EF-Tu
Molecular weight formula_weight	36966.3 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

GITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	TETRACYCLINE
Molecular weight formula_weight	444.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	2hdnB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnF03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnH03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnJ02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnJ03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2hdnL02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2hdnL03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

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Unit-cell length a length_a	69.710 Å
Unit-cell length b length_b	156.060 Å
Unit-cell length c length_c	134.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.1800
R_free r_free	0.2230

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

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

Elongation factor EF-Tu

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

2hdn__assembly_1__model_1

2hdn__assembly_1__model_1 | I(q)

2hdn__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

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

Elongation factor EF-Tu

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

2hdn__assembly_1__model_1

2hdn__assembly_1__model_1 | I(q)

2hdn__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)