SAXSdb — 9unm

▼

1. Structure Basics

entry_id	9unm
deposition_date	2025-04-23
title	native NMDA receptor-GluN1/N2A-S2 in the closed state
keywords	native, NMDA receptor, inotropic ion channel, excitatory neurotransmitter, MEMBRANE, open state, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	53.90 Å
rg_electron	53.89 Å
i0	1237030000.00
molecular_weight	287120.0 kDa
excluded_volume	356670 Å³
envelope_volume	587500 Å³
shell_volume	94057 Å³
envelope_diameter	177.6 Å
shell_rg	54.25 Å
envelope_rg	52.04 Å
shape_rg	53.88 Å
total_rg	53.94 Å
total_atoms	20267
n_residues	3150
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	183.2 Å
rg_real	53.84 Å
rg_real_error	1.93 Å
i0_real	1.2370e+09
i0_real_error	2.4450e+07
rg_reciprocal	53.94 Å
i0_reciprocal	1237000000.0000
total_estimate	0.8801
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.2 Å
skewness	0.256
kurtosis	-0.419
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	83400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.835

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glutamate receptor ionotropic, NMDA 1
formula_weight	91172.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	20267

VNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARDLEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCVDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAY

Entity 2 polymer

description	Glutamate receptor ionotropic, NMDA 2A
formula_weight	90616.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

PALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQTEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEH

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	11

Entity 4 non-polymer

description	(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
formula_weight	237.7 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	6.370 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	6.37 Å
resolution_method	—
num_particles	43792

fit	/app/data/saxs_computation/un/9unm/9unm.fit
pddf	/app/data/pr_computation/un/9unm/9unm.pr.out
profile	/app/data/saxs_computation/un/9unm/9unm.dat

native NMDA receptor-GluN1/N2A-S2 in the closed state

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)