SAXSdb — 8u86

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

NADPH oxidase 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–719 Chain C； UniProt 1–719	Not recorded	HEB HEME B/C × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 D12 DODECANE × 2 D10 DECANE × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8U86	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6SZ5 Human calmodulin bound to a peptide of human NADPH oxidase 5 Deposited 2019-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–737（719 aa） Chain C 19–737（719 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30 mM Tris-HCl at pH 7.4, 2.5 mM CaCl2 and 2.5% (v/v) glycerol	Resolution 2.23 Å R-free 0.294
8U7Y Structural Basis of Human NOX5 Activation Deposited 2023-09-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–719（719 aa） Chain B 1–719（719 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 D12 DODECANE × 2 D10 DECANE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 HEB HEME B/C × 4 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.06 Å
8U85 Structural Basis of Human NOX5 Activation Deposited 2023-09-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–719（719 aa） Chain C 1–719（719 aa）	Not recorded	HEB HEME B/C × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8U87 Structural Basis of Human NOX5 Activation Deposited 2023-09-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–719（719 aa） Chain C 1–719（719 aa）	Not recorded	HEB HEME B/C × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 1 D12 DODECANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.86 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NOX5_HUMAN
Isoform	Q96PH1-4
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–719； UniProt 1–719 Author chain C； PDBConstruct 1–719； UniProt 1–719

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	8u86
Deposition date deposition_date	2023-09-15
Structure title title	Structural Basis of Human NOX5 Activation
Keywords keywords	enzyme, oxidase, activation mechanism, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.34 Å
Radius of gyration Rg (electron density) rg_electron	32.39 Å
Forward intensity I(0) i0	169465000.00
Molecular weight molecular_weight	108250.0 kDa
Excluded volume excluded_volume	137140 Å³
Envelope volume envelope_volume	173360 Å³
Hydration-shell volume shell_volume	44324 Å³
Envelope diameter envelope_diameter	112.9 Å
Shell Rg shell_rg	39.53 Å
Envelope Rg envelope_rg	31.84 Å
Shape Rg shape_rg	32.34 Å
Total Rg total_rg	33.18 Å
Total atoms total_atoms	7623
Residues n_residues	892
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.6 Å
Rg (real space) rg_real	33.22 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.6950e+08
I(0) uncertainty (real space) i0_real_error	2.7170e+06
Rg (reciprocal space) rg_reciprocal	33.30 Å
I(0) (reciprocal space) i0_reciprocal	169500000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.4 Å
Skewness Skewness skewness	0.149
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25510000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	NADPH oxidase 5
Molecular weight formula_weight	82119.0 kDa
EC 编号 ec_number	1.6.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7623

MSAEEDARWLRWVTQQFKTIAGEDGEISLQEFKAALHVKESFFAERFFALFDSDRSGTITLQELQEALTLLIHGSPMDKLKFLFQVYDIDGSGSIDPDELRTVLQSCLRESAISLPDEKLDQLTLALFESADADGNGAITFEELRDELQRFPGVMENLTISAAHWLTAPAPRPRPRRPRQLTRAYWHNHRSQLFCLATYAGLHVLLFGLAASAHRDLGASVMVAKGCGQCLNFDCSFIAVLMLRRCLTWLRATWLAQVLPLDQNIQFHQLMGYVVVGLSLVHTVAHTVNFVLQAQAEASPFQFWELLLTTRPGIGWVHGSASPTGVALLLLLLLMFICSSSCIRRSGHFEVFYWTHLSYLLVWLLLIFHGPNFWKWLLVPGILFFLEKAIGLAVSRMAAVCIMEVNLLPSKVTHLLIKRPPFFHYRPGDYLYLNIPTIARYEWHPFTISSAPEQKDTIWLHIRSQGQWTNRLYESFKASDPLGRGSKRLSRSVTMRKSQRSSKGSEILLEKHKFCNIKCYIDGPYGTPTRRIFASEHAVLIGAGIGITPFASILQSIMYRHQKRKHTCPSCQHSWIEGVQDNMKLHKVDFIWINRDQRSFEWFVSLLTKLEMDQAEEAQYGRFLELHMYMTSALGKNDMKAIGLQMALDLLANKEKKDSITGLQTRTQPGRPDWSKVFQKVAAEKKGKVQVFFCGSPALAKVLKGHCEKFGFRFFQENF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	HEME B/C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DODECANE
Molecular weight formula_weight	170.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	201424

fit	/app/data/saxs_computation/u8/8u86/8u86.fit
pddf	/app/data/pr_computation/u8/8u86/8u86.pr.out
profile	/app/data/saxs_computation/u8/8u86/8u86.dat

Structural Basis of Human NOX5 Activation