SAXSdb — 2nwx

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

425aa long hypothetical proton glutamate symport protein

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 6 ASPARTIC ACID × 3 PALMITIC ACID × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59010_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–417； UniProt 1–417 Author chain B； PDBConstruct 1–417； UniProt 1–417 Author chain C； PDBConstruct 1–417； UniProt 1–417

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	2nwx
Deposition date deposition_date	2006-11-16
Structure title title	Crystal structure of GltPh in complex with L-aspartate and sodium ions
Keywords keywords	;amino acid transporter, transmembrane transporter, aspartate transporter, binding site, sodium binding, substrate binding, TRANSPORT PROTEIN ;; TRANSPORT 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.

2nwx__assembly_1__model_1

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

Download this curve (.dat)

2nwx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nwx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.02 Å
Rg (electron density)	33.33 Å
Total Rg	33.92 Å
Atom count	8593
Residues	1197
Excluded volume	157930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nwx__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	425aa long hypothetical proton glutamate symport protein
Molecular weight formula_weight	44641.9 kDa
Mutation mutation	D37H, K40H, K125H, K132H, K223H, K264H, E368H
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8596

MGLYRKYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGTLVPR

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2nwxa1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.49 — Proton glutamate symport protein
Superfamily Superfamily superfamily	f.49.1 — Proton glutamate symport protein
Family Family family	f.49.1.1 — Proton glutamate symport protein

Domain ID domain_id	d2nwxb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.49 — Proton glutamate symport protein
Superfamily Superfamily superfamily	f.49.1 — Proton glutamate symport protein
Family Family family	f.49.1.1 — Proton glutamate symport protein

Domain ID domain_id	d2nwxc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.49 — Proton glutamate symport protein
Superfamily Superfamily superfamily	f.49.1 — Proton glutamate symport protein
Family Family family	f.49.1.1 — Proton glutamate symport protein

CATH v4.4 (3 domains)

Domain ID domain_id	2nwxA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

Domain ID domain_id	2nwxB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

Domain ID domain_id	2nwxC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

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Unit-cell length a length_a	115.473 Å
Unit-cell length b length_b	115.473 Å
Unit-cell length c length_c	324.227 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.2650
R_work r_work	0.2630
R_free r_free	0.2860

Crystal structure of GltPh in complex with L-aspartate and sodium ions

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

425aa long hypothetical proton glutamate symport protein

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

2nwx__assembly_1__model_1

2nwx__assembly_1__model_1 | I(q)

2nwx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of GltPh in complex with L-aspartate and sodium ions

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

425aa long hypothetical proton glutamate symport protein

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

2nwx__assembly_1__model_1

2nwx__assembly_1__model_1 | I(q)

2nwx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)