6nle

X-ray structure of LeuT with V269 deletion

Method: X-RAY DIFFRACTION

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

Na(+):neurotransmitter symporter (Snf family)

Aquifex aeolicus (strain VF5)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	LEUCINE × 1 SODIUM ION × 2 GLYCEROL × 2 DI(HYDROXYETHYL)ETHER × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 octyl beta-D-glucopyranoside × 1 N-OCTANE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O67854_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–497； UniProt 4–508

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	6nle
Deposition date deposition_date	2019-01-08
Structure title title	X-ray structure of LeuT with V269 deletion
Keywords keywords	LeuT, MEMBRANE PROTEIN; MEMBRANE 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.

6nle__assembly_1__model_1

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

Download this curve (.dat)

6nle__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nle__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.14 Å
Rg (electron density)	22.05 Å
Total Rg	23.10 Å
Atom count	3920
Residues	491
Excluded volume	72435 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nle__assembly_1__model_1`	monomeric （1）	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 (9)

Entity 1 Entity 1 polymer

Description description	Na(+):neurotransmitter symporter (Snf family)
Molecular weight formula_weight	56454.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4000

KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRR

Source Source

Source organism organism	Aquifex aeolicus (strain VF5)
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	LEUCINE
Molecular weight formula_weight	131.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6nlea_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.54 — SNF-like
Superfamily Superfamily superfamily	f.54.1 — SNF-like
Family Family family	f.54.1.1 — SNF-like

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Unit-cell length a length_a	149.540 Å
Unit-cell length b length_b	86.140 Å
Unit-cell length c length_c	81.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.615 Å
Low-resolution limit resolution_low	76.256 Å
R factor r_factor	0.2262
R_work r_work	0.2244
R_free r_free	0.2598

X-ray structure of LeuT with V269 deletion

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

Na(+):neurotransmitter symporter (Snf family)

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

6nle__assembly_1__model_1

6nle__assembly_1__model_1 | I(q)

6nle__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

X-ray structure of LeuT with V269 deletion

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

Na(+):neurotransmitter symporter (Snf family)

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

6nle__assembly_1__model_1

6nle__assembly_1__model_1 | I(q)

6nle__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)