SAXSdb — 9pzw

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1. Structure Basics

entry_id	9pzw
deposition_date	2025-08-11
title	GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state
keywords	ligand-gated ion channel, NMDA, antibody, complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	59.73 Å
rg_electron	60.17 Å
i0	2104470000.00
molecular_weight	391050.0 kDa
excluded_volume	491950 Å³
envelope_volume	780280 Å³
shell_volume	113000 Å³
envelope_diameter	206.3 Å
shell_rg	58.28 Å
envelope_rg	59.24 Å
shape_rg	60.16 Å
total_rg	60.12 Å
total_atoms	27525
n_residues	3493
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

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3. P(r) Analysis (GNOM)

dmax	204.8 Å
rg_real	59.78 Å
rg_real_error	2.37 Å
i0_real	2.1040e+09
i0_real_error	4.0510e+07
rg_reciprocal	59.65 Å
i0_reciprocal	2104000000.0000
total_estimate	0.8690
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.0 Å
skewness	0.339
kurtosis	-0.400
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	147500000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.720

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
formula_weight	15448.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,L
atom_count	27525

MVSAIVLYVLLAAAAHSAFAQVQLQQSGAELMKPGASVKISCKATGYTFRSYWIEWLKQRPGHGLEWIGEILPGSGRTNYNEKFKGKATITADTSSNTAYMQLSSLTSEDSAVYYCTRSRGTMITREFTYWGQGALVTVSA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
formula_weight	13989.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,M

MVSAIVLYVLLAAAAHSAFADIVLTQSPASLAVSLGQRATISCRASESVEYYGTTLMQWYQQKPGQPPKLLIYAASNVDSGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSRKVPSTFGGGTKLEIK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	Glutamate receptor ionotropic, NMDA 1
formula_weight	95372.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C

MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQ

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 4 polymer

description	Glutamate receptor ionotropic, NMDA 2A
formula_weight	97163.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MGRLGYWTLLVLPALLVWRDPAQNAAAEKGPPALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQAEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFCFTGVCSDRPGLLFSISRG

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 5 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	16

Entity 7 non-polymer

description	GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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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	3.430 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.43 Å
resolution_method	—
num_particles	183438

fit	/app/data/saxs_computation/pz/9pzw/9pzw.fit
pddf	/app/data/pr_computation/pz/9pzw/9pzw.pr.out
profile	/app/data/saxs_computation/pz/9pzw/9pzw.dat

GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound 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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)