SAXSdb — 6odl

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

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	(1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3V9C5_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 139–279； UniProt 504–644 Author chain B； PDBConstruct 139–279； UniProt 504–644

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

Rattus norvegicus

UniProt Q00959

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	(1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMDE1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 404–539 Author chain B； PDBConstruct 1–136； UniProt 404–539

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	6odl
Deposition date deposition_date	2019-03-26
Structure title title	Crystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV
Keywords keywords	NMDA RECEPTOR, ANTAGONIST, TRANSPORT PROTEIN, RECEPTOR; 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.

6odl__assembly_1__model_1

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

Download this curve (.dat)

6odl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6odl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.44 Å
Rg (electron density)	25.36 Å
Total Rg	26.29 Å
Atom count	4420
Residues	557
Excluded volume	79059 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6odl__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
Molecular weight formula_weight	31353.9 kDa
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	4596

NHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid
Molecular weight formula_weight	215.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6odla_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

Domain ID domain_id	d6odlb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.0 — automated matches

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Unit-cell length a length_a	52.094 Å
Unit-cell length b length_b	52.094 Å
Unit-cell length c length_c	197.804 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.026 Å
R factor r_factor	0.2294
R_work r_work	0.2243
R_free r_free	0.2827

Crystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV

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

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

State in the Current Structure

Other States of the Same Protein in the Database

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

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

6odl__assembly_1__model_1

6odl__assembly_1__model_1 | I(q)

6odl__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV

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

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

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

6odl__assembly_1__model_1

6odl__assembly_1__model_1 | I(q)

6odl__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)