SAXSdb — 9pzt

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1. Structure Basics

entry_id	9pzt
deposition_date	2025-08-11
title	Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
keywords	ligand-gated ion channel, NMDA, antibody, native, 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	59.82 Å
rg_electron	59.06 Å
i0	1742910000.00
molecular_weight	345230.0 kDa
excluded_volume	429120 Å³
envelope_volume	704940 Å³
shell_volume	102030 Å³
envelope_diameter	203.8 Å
shell_rg	58.90 Å
envelope_rg	58.01 Å
shape_rg	59.12 Å
total_rg	58.83 Å
total_atoms	24381
n_residues	3446
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	202.8 Å
rg_real	59.82 Å
rg_real_error	2.01 Å
i0_real	1.7430e+09
i0_real_error	3.7130e+07
rg_reciprocal	59.80 Å
i0_reciprocal	1743000000.0000
total_estimate	0.8190
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.2 Å
skewness	0.293
kurtosis	-0.429
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0001
highest_alpha	103800000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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	L,J
atom_count	24381

MVSAIVLYVLLAAAAHSAFAQVQLQQSGAELMKPGASVKISCKATGYTFRSYWIEWLKQRPGHGLEWIGEILPGSGRTNYNEKFKGKATITADTSSNTAYMQLSSLTSEDSAVYYCTRSRGTMITREFTYWGQGALVTVSA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

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	M,K

MVSAIVLYVLLAAAAHSAFADIVLTQSPASLAVSLGQRATISCRASESVEYYGTTLMQWYQQKPGQPPKLLIYAASNVDSGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSRKVPSTFGGGTKLEIK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Glutamate receptor ionotropic, NMDA 2A
formula_weight	165619.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,B

MGRLGYWTLLVLPALLVWHGPAQNAAAEKGTPALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQTEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFCFTGVCSDRPGLLFSISRGIYSCIHGVHIEEKKKSPDFNLTGSQSNMLKLLRSAKNISNMSNMNSSRMDSPKRAADFIQRGSLIVDMVSDKGNLIYSDNRSFQGKDSIFGENMNELQTFVANRHKDSLSNYVFQGQHPLTLNESNPNTVEVAVSTESKGNSRPRQLWKKSMESLRQDSLNQNPVSQRDEKTAENRTHSLKSPRYLPEEVAHSDISETSSRATCHREPDNNKNHKTKDNFKRSMASKYPKDCSEVERTYVKTKASSPRDKIYTIDGEKEPSFHLDPPQFIENIVLPENVDFPDTYQDHNENFRKGDSTLPMNRNPLHNEDGLPNNDQYKLYAKHFTLKDKGSPHSEGSDRYRQNSTHCRSCLSNLPTYSGHFTMRSPFKCDACLRMGNLYDIDEDQMLQETGNPATREEAYQQDWSQNNALQFQKNKLKINRQHSYDNILDKPREIDLSRPSRSISLKDRERLLEGNLYGSLFSVPSSKLLGNKSSLFPQGLEDSKRSKSLLPDHTSDNPFLHTYGDDQRLVIGRCPSDPYKHSLPSQAVNDSYLRSSLRSTASYCSRDSRGHSDVYISEHVMPYAANKNNMYSTPRVLNSCSNRRVYKKMPSIESDV

Entity 4 polymer

description	Glutamate receptor ionotropic, NMDA 1
formula_weight	105617.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,A

MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARDLEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCVDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQDRKSGRAEPDPKKKATFRAITSTLASSFKRRRSSKDTSTGGGRGALQNQKDTVLPRRAIEREEGQLQLCSRHRES

Entity 5 polymer

description	Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
formula_weight	29432.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,F

MVSAIVLYVLLAAAAHSAFAQGQMQQSGAELVKPGASVKLSCKTSGFSFSTSYINWLKQKPGQSLEWIAWIYAGTDGTSYNQKFTDKAQLTVDTSSSTAYMQFSSLTTDDSAIYYCAREGIYYGNYAGFTYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKLVPRGSAAAAGTGSGGGDYKDHDGDYKDHDIDYKDDDDK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
formula_weight	26910.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,G

MVSAIVLYVLLAAAAHSAFADIVMTQSPSSLAVTAGEKVTMRCKSSQSLLWSVNQNNYLSWYQQKQGQPPKLLIYGASIRESWVPDRFTGSGSGTDFTLTISNVHAEDLAVYYCQHNHGSFLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECSN

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

Entity 7 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

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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	6.140 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	6.14 Å
resolution_method	—
num_particles	26341

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

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), 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

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)